Abstract: From Paleozoic to Mesozoic, multiple types of basins developed in the Lower Yangtze region, forming 2 sets of petroleum assemblages of marine facies (the lower one and the upper one). Influenced by the tectonic deformation and basin superposition during Indosinian-middle Yanshanian and late Yanshanian-Himalayan periods, the generation, evolution, migration and accumulation of petroleum in marine strata are very complicated. As a result, it is difficult to select favorable zones for petroleum exploration in traditional ways. Based on the theory of “source and cap rocks control hydrocarbon”, the relationships between hydrocarbon kitchen and cap rock at the end of Caledonian, the end of Indosinian, the end of middle Yanshanian and present days are discussed, and the favorable zones for petroleum accumulation and preservation are predicted. An accumulation prediction model of multiple layers, stages and elements is applied to point out favorable zones for exploration.