Grain size analysis, magnetism analysis, pollen analysis and chronology analysis are performed on the samples from Longqiuzhuang Site of Gaoyou, and Qingdun Site of Hai'an in the north part of the Yangtze Delta, analyzing the relationship between rise and fall of human civilization and environment changes. The research result indicates that before human settlement occurred in the study region, the ocean is relatively far away from the region but influenced frequently by the high tide. The warm and wet climate occurred in 7000-6000 a B. P. and around 3700 a B. P. in the study region. The comfortable climatic conditions were suitable for human settlement and human civilization. It should be mentioned that, about 1m natural sedimentary layer is contained in the Qingdun profile. Grain size and pollen analysis suggest that this natural layer is the result of marine transgression event occurred after 4000 a B. P., and just this great transgression event caused the human civilization in this study region collapsed. This paper applied sediment deposition from two Neolithic sites: Longqiuzhuang Site of Gaoyou and Qingdun Site of Hai'an in the study of correlation between rise and fall of human civilization and climatic changes during the Neolithic cultural period, avoiding the uncertainty in the archaeological study applying just one site profile. Therefore, the research is theoretically and practically meaningful.