Abstract: The exploration of oil and gas in Southwest Bozhong Sub-depression shows that the enrichment degree of hydrocarbon is different in different reservoirs, since the difference in oil sources. In order to find out the control factors of hydrocarbon accumulation and effective exploration targets, we studied the relationship between troughs and source rocks based on a thorough study of the structural features of different kinds of troughs, and a comprehensive evaluation method is summarized and presented. Up to date, four types of troughs are recognized in the region, namely the inherited fault trough, the early decline fault trough, early decline fault and overlapping trough, and inherited fault and overlapping trough. The differences of trough evolution also control the evolution of source rock, and determined the main source rock formation and the advantages of migration direction, finally lead to great disparities of hydrocarbon source in different structures. According to the study, we succeedly optimized the exploration targets in the Southwest Bozhong Sub-depression.