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The Central Plains has a long history, rich culture, unique geographical advantages, and profound cultural heritage. The occurrence of ancient cities in the Central Plains marks the formation of Chinese state-level societies. The number, size, and distribution of ancient cities have changed greatly from the late Yangshao to the Xia and Shang Dynasties, which reflects the evolution of settlement and social organization. In this study, Geographic Information System (GIS) spatial database technology was used to establish a spatiotemporal database of ancient cities in the late Yangshao, Longshan, as well as Xia and Shang Dynasties in the Central Plains. This paper uses GIS spatial analysis technology to analyze the relationship between the ancient city distribution and the geographical environment, as well as the evolution of ancient city's shapes and sizes. Furthermore, by using the method of the nearest neighbor distance and gravity center analysis, this paper discusses the agglomeration characteristics and gravity center evolution of ancient cities. The results show that: (1) Most of the ancient cities were distributed in areas below 500 m and within 3 km from the river during the time interval from the late Yangshao to Xia and Shang Dynasties; (2) The shape of the ancient cities gradually changed from circles to squares in the Central Plains, which became a unified model for the later ancient city design; (3) The sizes of the 18 ancient cities in the Yangshao period shared high similarity, with an average area of 20 hectares. The sizes of 24 ancient cities in the Longshan period increased significantly, with an average of 39 hectares. During the Xia and Shang Dynasties, there were 22 ancient cities with an average size of 340 hectares, and the grade of sizes became obvious, marking the entrance into Chinese state-level societies; (4) Cities were scattered in the decentralized pattern during the late Yangshao and Longshan periods, whereas they became agglomerative in Xia and Shang Dynasties. This reflects the evolution of the spatial scopes and social organizational forms; and (5) From the late Yangshao to Xia and Shang Dynasties, the gravity center of ancient cities moved around the Songshan Mountain from the northwest to the southeast and again to the northeast.