The sediment transport process in watersheds is an important research component of geomorphology and surface dynamics. Previous work has inferred the spatial distribution of the sediment transport rate (STR) by the flow direction algorithm and measured topographic variation; however, the simple application of the flow direction algorithm contributes to mass non-conservation during a simulation. This study designs an improved flow direction algorithm for a sediment transport process simulation by judging the mass conservation situation in the simulation process. The specific implementation is to evaluate the existence of negative values for the STR; if they exist, the negative values of the STR are reset to stop the propagation of the negative values downstream. Experiments are conducted to improve the classical D8, MFD–se, and MFD–md flow algorithms in this paper, and the experimental results show that the method in this paper can effectively improve the simulation effect of STR. The STR simulations of the three models, D8, MFD–se, and MFD–md, improved by 1.26%, 4.17%, and 4.54%, respectively. Moreover, the MFD–se model is more suitable for the simulation of the STR when comparing the three models. The improved flow algorithm can be used to simulate the STR, sediment content, and pollutant migration in watersheds, providing a new method for the fine-grained characterization of surface processes in watersheds.