Abstract: The early Neolithic sites in Anhui Province include Xiaoshankou in the area north of the Huaihe River and Gouting in the area south of the Changjiang(Yangtze) River. The wild animal bones and pollen analysis from middle Neolithic age sites excavating show there are rivers, lakes, forest and grassland around the sites. The sites distribution of the late Neolithic age illustrates that, the ancients had able to distinguish the soil quality and to use environment condition to improve the soil. The profile analysis for Yuchisi Site, Mengcheng County shows that, environment was only the basic factor for ancient sites disitribution and quantity change, the productivity factors were also operated. In Xia-Shang-Zhou dynasties, the total number of sites in the whole province increased, but that in Huaibei Plain reduced on a large scale, for which the reson was air temperature continually drop and the flood invaded in the early Xia Dynasty. By popular highland landform, middle and south Anhui suffered only light flood effect, and after flood, the sites recoveray and development were rapid in these area. Most new sites were built in the place which were advantageous to agricature production and avoiding flood disaster.