The computing model of Dynamic Watershed Simulation Model(DWSM) has some limitations, such as low robustness, long computing time, and inability to realize failure in a multicore computer. Therefore, in this paper, we improved the algorithms and storing rules. Based on the computational logic sequence of DWSM, we suggest to use the concept of basin subarea to design the tree structure model of river network instead of the hypothesis on virtual channel of the original calculation unit sequence table model. Also, we introduce the dynamic hierarchical parallel computing technology according to parallel computation of leaf nodes to improve the calculation model. Taking the Yellow River basin between Ningxia and Neimenggu as an example, the results show that the optimization of algorithm greatly improves the computational efficiency of DWSM as well as increases the applicability of calculation on water and sediment rules in the basins with large scale and complex structure of river network.