Lacustrine source rocks are widely distributed in the Mesozoic rift basins of northern China. Two lacustrine rift sub-depressions in the Suhongtu depression, Yin-E Basin, have been subjected to a comprehensive analysis of their source rock potential to further reveal the controlling factors and enrichment mechanisms by constructing models for lacustrine source rocks in different tectonic settings. The Hari sag in the Suhongtu depression has significantly greater sedimentary cover and better hydrocarbon generation conditions when compared to the Babei sag by comprehensive analyses of total organic carbon (TOC), chloroform bitumen “A”, Rock-Eval pyrolysis and δ13CPDB. The results show that source rock deposition was affected by organic productivity, organic matter preservation and sedimentation rates. The TOC and δ13CPDB values indicate that there was higher productivity in the lakes of the Hari sag, and productivity reached a maximum during the deposition of the Yingen Formation. The total reduced sulphur (TRS), Pr/Ph, and gammacerane index values indicate that a relative reducing environment was present in the Hari sag. During deposition of the Bayingebi Formation in the Hari sag, the water was suboxic-anoxic, gradually turning anoxic and finally formed a strongly reducing, high-salinity, stratified water environment during deposition of the Yingen Formation. The Babei sag was suboxic-oxidizing throughout the deposition of the Lower Cretaceous lacustrine mudstones. With more active boundary faults and higher sedimentation rates, the terrigenous organic matter inputs to the Hari sub-depression were higher than those in the Babei sub-depression. These observations permitted the development of a model for the formation mechanism for the effective lacustrine source rocks in the Cretaceous fault basin of the Suhongtu depression. In the Hari sag, during source rock deposition of the K1b and K1s formations, intense and more active faults resulted in high terrigenous organic matter being carried into the lake. However, rapid sedimentation rates caused organic matter dispersed. During source rock deposition of the K1y Formation, the sag entered a transition stage from synrift to post-rift with an intermediate sedimentation rate. More organic matter was continuously transported into the basin with high salinity and a strongly reducing sedimentary environment, which caused enrichment of organic matter. In the Babei sag, due to small-scale rifting structures and shallow water conditions, a relatively low influx of terrigenous organic matter and suboxic to oxidizing conditions were developed. This study have important implications for source rock prediction in other lacustrine rift basins.