The Doubthouse climate is a typical cooling climate between the Early Eocene Climate Optimum (EECO) and the Middle Eocene Climate Optimum (MECO). The precise timing of this climate’s occurrence and its effects on the carbon cycle and organic matter enrichment remain unknown. This work studied the upper 4th Mbr of Shahejie Fm in the Eocene Dongpu Depression (DD), Bohai Bay Basin, to reveal the controlling effect of the Doubthouse climate on organic matter enrichment. The astronomical time scale (ATS) of the upper 4th Mbr of Shahejie Fm in the DD is established as 41.38–43.31 Ma (±0.1 Myr) using a natural gamma logging curve. The simulated sedimentation rate is 14.6 cm/kyr. The organic matter is mostly from freshwater algae such as green algae, cyanobacteria, and dinoflagellates. The positive excursion (4.07 ‰) of δ13C corresponds to the increased weathering intensity and the humid climate, which benefit algae growth. The paleo-productivity and sedimentation rates during the Doubthouse climate period increased. Besides, the cooling climate inhibited the respiration of the algae. Therefore, CO2 intake > organic carbon consumption was recorded as δ13C excursion. Hence, we propose that the doubthouse climate is the controlling factor of organic matter enrichment.