The pollen, phytolith and geochemistry analysis results of the Xuecheng Neolithic relics and the Sanxing-cun Neolithic relics in the Yangtze River Delta show the relationship between the rise and fall of prehistoric cultural and climatic change. The Xuecheng Neolithic relics is the earliest Neolithic site in the Nanjing region. After Younger Dryas, temperature rose continuously till the Holocene Hypsithermal. The climate was sustained, which made the Neolithic culture developed. The Sanxincun site spanned from the middle stage of the Majia-bang culture to the middle stage of the Songze culture. Prior to 5000 a BP, the climate was humid and warm. Nevertheless, at the end of the Songze culture, the climate became cold and dry, and the natural environment was severely damaged. At that time the Songze culture vanished.