[The] Hamin Mangha site is the largest and best-preserved prehistoric settlement site found to date in northeast China[.]The community also had at least 29 one room houses with doors and hearths. The village's population couldn't have been more than a few hundred, yet it lost almost a hundred souls in what must have been a matter of days or weeks at most. An abstract of a 2011 paper on the site clarifies that it was located in Inner Mongolia.
The ages of the victims at Hamin Mangha are similar to those found in another prehistoric mass burial, which was previously unearthed in modern-day Miaozigou in northeast China, the researchers noted. . . . "This similarity may indicate that the cause of the Hamin Mangha site was similar to that of the Miaozigou sites. That is, they both possibly relate to an outbreak of an acute infectious disease," wrote Zhou and Zhu.A poster abstract from an anthropology conference is here and indicates that there was a third similar site in the region as well. It is also similar to a northeast China site at Lajia, which is also the site were the oldest evidence of noodles in China (ca. 2000 BCE and made of millet) were discovered.
The researchers didn't offer speculation on what disease, if any, may have been involved in the two cases. But, any disease that killed so rapidly that this kind of mass grave and burning to prevent spread of the disease could have had powerful demographic effects and left traces behind in modern populations through selection on genes that confer resistance to it.
The Neolithic culture of that time period in Inner Mongolia was the late Hongshan culture (4700 BCE to 2900 BCE), which interacted with the larger contemporaneous but separate Yangshao culture. Remains from the Hongshan culture are associated with Y-DNA N1 (xN1a, Nic), C and O3a (O3a3). There is dispute over whether these people spoke a language in the same language family as Chinese.
Unlike almost all other historical Chinese cultures, they had an elaborate temple based goddess worship system, were known for jade artifacts depicting pregnant women, dragons, and tortoises, and are believed to be the original source of the Feng Shui mystical system. They had small copper rings, although they were not necessarily a full fledged copper age civilization.
This would have happened long after the domestication of rice and millet, but not long before the rapid expansion of rice farming into mainland Southeast Asia, India and Nepal. It was before written records are available. A millet and pig based diet like the neighboring Yangshao culture seems likely, although hunting and fishing may have played a major part as well.
A warm period known as the Holocene Climate Optimum, from ca. 7000 BCE to 3000 BCE was just ending when this disaster struck, and it may have been harder to survive this climate transition in an inland relatively high altitude area like Inner Mongolia, than in places that stayed relatively warm like coastal China or Southern China.
During the Holocene Climate Optimum, "Current desert regions of Central Asia were extensively forested due to higher rainfall and the warm temperate forest bets in China and Japan were extended northwards." It appears that this civilization collapsed due to rapid expansion of northern deserts into its territories possibly forcing its people to migrate to the south.
[R]ivers and lakes once dominated the region’s terrain, and that relatively deep water existed there between 5,000 and 9,000 years ago, along with vegetation including spruce, fir, birch, pine and oak trees. Beginning about 4,200 years ago, the researchers found, a dramatic transformation occurred. According to their findings . . . more than 7,770 square miles (20,000 square km) of the Hunshandake area rapidly dried up and turned into desert. The scientists suggest that a river permanently diverted water from the region, around the same time that a major climactic shift worldwide created severe droughts on all the continents in the Northern Hemisphere. As study co-author Louis Scuderi, a paleoclimatologist at the University of New Mexico in Albuquerque, told LiveScience: “We think this drying happened in northern China as well, but was augmented by massive amounts of water getting diverted away from the area.”The event would have been similar to the sudden diversion and drying up of the Saravasti River in Northern India that brought about the collapse of the Harappan civilization. Those events in India were accompanied by leprosy, TB and intracommunity violence.
The infectious disease in the case of this Chinese mass immolation must have been much more virulent than either leprosy or TB to cause so many deaths so quickly. This occurred before the earliest attested small pox infestation in China. But, this could simply be due to the lack of historical records, as it was recorded in China as far back as 1122 BCE, close in time to the dawn of the Chinese historical record, and small pox is both highly contagious and has a very high mortality rate. Plague proper also shares those features but there aren't known examples of it that are so ancient. Still, this site has some similarities to "plague pits" in Europe. Anthrax has high enough mortality, is ancient, and can be associated with pigs, but seems to be only rarely associated with large historical outbreaks that would spread across several villages.
This site does not resemble a mass grave of 80 young women from 2000 BCE found in Shaanxi province in China, discovered in 2012, that was probably the site of a human sacrifice ritual.
This disaster coincides in time with the late Neolithic transition in the Yellow River valley from the Yangshao culture (5000 BCE to 3000 BCE) and the Longshan culture (3000 BCE to 2000 BCE) and the roughly contemporaneous Liangzhu culture (3400 BCE to 2250 BCE). It seems likely that a plague like the one in Inner Mongolia could have been intimately related to the parallel events that produced this transition between archaeological cultures on the Yellow River in addition to the collapse of their own culture.
The descriptions of the Hongshan site in the news report seem more like that of the Yangshao culture or Longshan culture than the more sophisticated Liangzhu culture. Both of those cultures experienced rather dramatic collapses. The collapse of the Liangzhu culture was particularly sudden and mysterious (but too late and too far away to be connected to the site where the bodies were found). The collapse of the Longshan culture is described as follows in Wikipedia:
[T]he Neolithic population in China reached its peak during the Longshan culture. Towards the end of the 3rd millennium BC, the population decreased sharply in most of the region and many of the larger centres were abandoned, possibly due to environmental change linked to the end of the Holocene Climatic Optimum. This was matched by the disappearance of high-quality black pottery found in ritual burials. In contrast, there was a rapid growth of population and social complexity in the basin of the Yi and Luo rivers of central Henan, culminating in the Erlitou culture. The material culture in this area shows a continuous development, through a Xinzhai phase centred on the Song Mountains immediately to the south. In the Taosi area, however, there is no such continuity between Longshan and Erlitou material culture, suggesting a collapse in that area and later expansion from the Erlitou core area.The Erlitou culture was the earliest Bronze Age culture of China.
Both the Yangshao culture and the Longshan culture had primarily millet, pig and dogs as sources of sustenance, cultivated silkworms, and had minor use of rice, with few cattle, sheep or goats.