The variation of carbon and oxygen isotopes composition of carbonate rock is highly indicative of the sedimentary environment，water salinity，and climate change of lake basins. The lake shale of Lower Es3（the Lower Submember of the 3rd Member of Eocene Shahejie Formation）and Upper Es4（the Upper Submember of the 4th Member of Eocene Shahejie Formation）in Bonan Sag was studied，according to the on-line analysis method of the carbon and oxygen isotopes of trace carbonate rock. The results show that δ13CPDB and δ18OPDB in Upper Es4 are both negative，and are positively correlated. It indicated a closed brackish lacustrine environment with a high temperature during the development of fault depression. The negative deviation of δ13CPDB was not only influenced by freshwater supply but also related to the high sulfate content in the lake during the sedimentary period. The light δ18OPDB resulted mainly from the cementation in the middle-late period of diagenesis.The δ13CPDB and δ18OPDB in Lower Es3 were relatively heavy and well correlated，which implied that the lacustrine environment during the peak period of fault depression was hydrologically closed and stable. The variation of carbon and oxygen isotopes of carbonate rocks in the longitudinal direction indicated a shift from a relatively dry climate to a warm and humid climate during the early to late sedimentation.Meanwhile，the water salinity gradually decreased.