Based on the analysis of the hydrocarbon geochemical characteristics in the Kuqa petroleum system of the Tarim Basin, this study discusses the causes and controlling factors of the phase diversities and their differences in geochemical features. According to the characteristics and differences in oil and gas phase, the petroleum system can be divided into five categories: oil reservoir, wet gas reservoir, condensate gas-rich reservoir, condensate gas-poor reservoir and dry gas reservoir. The causes for the diversities in oil and gas phases include diversities of the sources of parent material, maturity of natural gas and the process of hydrocarbon accumulation of different hydrocarbon phases. On the whole, the Jurassic and Triassic terrestrial source rocks are the main sources for the hydrocarbon in the Kuqa Depression. The small differences in parent material may cause diversities in oil and gas amount, but the impact is small. The differences in oil and gas phase are mainly affected by maturity and the accumulation process, which closely relates with each other. Oil and gas at different thermal evolution stage can be captured in different accumulation process.