Estimation of base level changes in geological records is an important topic for petroleum geologists. Taking the Paleocene Upper Lingfeng Member of Lishui Sag as an example, this paper conducted a base level reconstruction based on Basin Filling Modelling (BFM). The reconstruction was processed on the ground of a previously interpreted seismic stratigraphic framework with several assumptions and simplification. The BFM is implemented with a nonlinear diffusion equation solver written in R coding that excels in shallow marine stratigraphic simulation. The modeled results fit the original stratigraphy very well. The BFM is a powerful tool for reconstructing the base level, and is an effective way to check the reasonableness of previous interpretations. Although simulation solutions may not be unique, the BFM still provides us a chance to gain some insights into the mechanism and dynamic details of the stratigraphy of sedimentary basins.