The Zhanmatun site is located in the southern suburb of Zhengzhou city, Henan Province, Shibalihe town. From 2009 to 2010, the Zhanmatun site was excavated by Henan Provincial Institute of Cultural Relics and Archaeology with rich remains of the Qinwangzhai culture (3900 BC~2900 BC) were found in the western area of the site. To analyze the composition of human population of Qinwangzhai culture at the site, 45 relatively complete skulls (25 males, 20 females) were observed and measured. Craniofacial morphology of the skulls was compared with other skull groups of different archaeological cultures in prehistoric age by applying cluster analysis and multidimensional scaling of Euclidean distances. Results show that Zhanmatun craniofacial morphology is closest to skull groups of the Qinwangzhai culture in Zhengzhou, such as the Wanggou and Xishan group, and also has many similarities with the Xixiahou group of Dawenkou culture (4200 BC~2600 BC). All these skull groups in the Qinwangzhai and Dawenkou cultures show occipital deformation and tooth extraction. The Zhanmatun craniofacial morphology group differs greatly from groups in center distribution area of the Yangshao culture (4900BC~2700BC). The central distribution area of Yangshao culture and peripheral remains have different connotations and sources. The Qinwangzhai culture (or Dahe Village culture) belongs to these peripheral remains, mainly distributed in the central area of Henan with Songshan Mountain as its center. This may indicate that different archeological and cultural factors may be the reason for the great difference in skull groups in the two distribution areas. Moreover, it means that in about 3000 BC, the influence and expansion of Dawenkou culture on the Central Plains was not limited to the eastern and southeastern areas of Henan, and the spread of culture and migration of people had already extended to the central area of Henan where the Zhanmatun site is located. There are some differences between males and females in Zhanmatun, with males similar to the Longqiuzhuang group in Jianghuai, and females similar to the Jiangjialiang group in North China. The first reason is that the Dawenkou culture, Longqiuzhuang culture (6600~5000 BP) and Dahe village culture have a common source, namely the Peiligang culture (6200 BC~5500 BC). The second reason is that the ancient North China type represented by Jiangjialiang residents reflects genic and cultural exchanges between the ancient Central Plains type in the late Yangshao period and the original residents of the northern Great Wall area suggesting that the genes of the northern people were also mixed into the Zhanmatun population. On the whole, although craniofacial features of Zhanmatun group are mostly common, there are a few differences, and the population composition is of multi-origin and integration that is consistent with obvious characteristics of the complex and multiple factors of Qinwangzhai culture.