This paper is the result of hydrogeological survey engineering.[Objective] The formation and evolution of the Yangtze River and the recurrent flood disasters in the middle and lower reaches of the Yangtze River are the key scientific problems to be solved urgently. [Methods] By using alluvial fan genetic theory, combined sedimentary facies profile correlation method, lithofacies paleogeographic analysis, high-precision dating technology, remote sensing method and so on, from the perspective of the basin, the genesis of gravel layers and lithofacies paleogeographic characteristics along the middle and lower reaches of the Yangtze River, planation surface and terrace characteristics of the Three Gorges and the genesis of the great turn of Yangtze River in Shigu, Yunnan in the upper reaches of the Yangtze River are analyzed. [Results] The understandings of the east-west transconnection time of the Yangtze River at the turn of early-Middle Pleistocene (750,000 years ago) and the Holocene river lake evolution pattern of "one River (Yangtze River) and four lakes (Yunmengze, Penglize, Dongting lake and Poyang Lake)" in the middle reaches of the Yangtze River the are put forward. The present situation and influencing factors of flood disaster in the middle and lower reaches of the Yangtze River in modern times under the natural and man-made effects were analyzed, and the evolution law of the Yangtze River and its enlightenment to flood disaster prevention and control were combined. The prevention and control measures of flood disaster in the middle and lower reaches of the Yangtze River including "rebuilding Yunmengze, expanding Dongting Lake and Poyang Lake", "Sand exploiting expansion lake, removing silt and turned into farmland" and relevant geological suggestions for the next step were put forward. [Conclusions] The major adjustment of geological environment in the early and middle Pleistocene was an important reason for the connection of the east and west lines of the Yangtze River. The flood disaster prevention and control in the middle reaches of the Yangtze River should fully consider the evolution law of rivers and lakes. The research results can provide basic support and theoretical basis for the territorial space planning, geological disaster prevention and ecological environment protection and restoration of the Yangtze River Economic Belt/Yangtze River Basin.