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Studies on basin fills have provided significant insights into reservoir distribution and prediction in petroliferous basins, however, the effect of basin fills on source rock properties has been underexplored. This paper documents basin filling characteristics and their implications for depositional processes and heterogeneity of source rock in the Qingnan subsag of the Jiuquan Basin, by using subsurface geological data from recent hydrocarbon exploration efforts in this area. Drill core data reveals that the basin fill of the Qingnan subsag was dominated by fan delta-lacustrine systems, in which deposition of the fan deltas along the basin margin was mainly through gravity flows. The temporal and spatial evolution of the depositional systems indicates that the basin fill was characterized by a continuously retrogradational process, with decreasing extent of fan deltas in vertical succession. Weakening of tectonic activities and climate change from humid to semi-arid are interpreted to be the main control factors that were responsible for the retrogradational basin fill. The different depositional environments in the early stage and late stage of the retrogradational basin filling history resulted in the different depositional processes and properties of source rocks. This study suggests that source rock heterogeneity associated with basin fills in lacustrine basins should be considered in hydrocarbon exploration.