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Deep and ultra-deep layers in the petroliferous basins of China are characterized by large temperature difference and complicated thermal evolution history. The control effects of temperature and thermal evolution history on the differences of hydrocarbon phase states and the hydrocarbon generation history in deep and ultra-deep layers are researched less and unsystematically. To deal with this situation, based on a large number of temperature and pressure data of deep layers and combined with the complicated historical situation of deep layer evolution in the oil and gas basins of China, the effects of temperature, heating time and pressure on the hydrocarbon formation temperature and phase state were analyzed, and the types of temperature and pressure relationships were classified. Finally, based on the classification of thermal evolution history of deep and ultra-deep layers, We discussed the control effects of basin thermal evolution history on the hydrocarbon generation and phase state, and the following research results were obtained. First, the hydrocarbon phase states of deep layers in different basins and regions are greatly different, and they are mainly affected by temperature, heating time, heating rate, pressure, source rock types and other factors. And temperature is the most important factor controlling hydrocarbon generation and phase state distribution. Second, under the conditions of rapid temperature increasing and short heating time, there still may be oil reservoirs and condensate gas reservoirs in deep and ultra-deep layers in the case of high temperature. Third, overpressure inhibits hydrocarbon generation and pyrolysis. Fourth, there is a close relationship between temperature and formation pressure of deep layers, which can be divided into three types, i.e., low–medium temperature and high pressure type, high temperature and high pressure type, and medium temperature and low–medium pressure type. Fifth, the thermal evolution history of deep and ultra-deep layers can be divided into four types, namely the late rapid subsidence, heating and low geothermal gradient type, the late rapid subsidence, heating and high geothermal gradient type, the middle–late rapid heating and late uplifting and cooling type, and the early great subsidence and rapid heating and middle–late great uplift erosion and cooling type. In conclusion, deep and ultra-deep layers in the basins with different types of thermal history are different in hydrocarbon phase states, accumulation stages and prospects.