The Bohai Bay Basin is the largest Cenozoic rift basin in eastern China, which exhibits a high rate of post‐rift subsidence deviating from the theoretical exponentially decay trend of thermal subsidence. The driving force for this phenomenon remains an outstanding question. Here we quantify the spatial and temporal distribution of the anomalous post‐rift subsidence by removing the thermal subsidence related to earlier stretching events from the observed tectonic subsidence. A multi‐episodic finite extension model is employed to estimate the stretching factors during rifting for nine profiles and 48 wells covering the basin. Our results show that the anomalous subsidence commenced at 12 Ma and the average anomalous subsidence rate accelerated from ∼19 m/Myr during the late Miocene to ∼75 m/Myr during the Quaternary, reaching ∼400 m at present. The anomalous subsidence is compared with published changes in dynamic topography arising from mantle flow. The temporal evolution of the dynamic topography generally fits the evolution of the anomalous subsidence, whereas variation in dynamic topography exhibits smaller amplitude and larger wavelength than our results. Small‐scale convection in the shallow mantle might play a role in generating short‐wavelength topography disturbances in the past tens of million years. Besides, the spatial distribution of the Quaternary anomalous subsidence generally coincides with fault movements in the past ∼2 Myr. We suggest mantle processes as well as fault activities might be possible mechanisms accounting for additional accommodation in the basin.