Urban rainwater storage tanks are one of the major engineering measures taken to solve urban waterlogging and improve the capacity of drainage system; however the existing operational rules for regulating storage tanks mostly focused on single tank operations. In view of this, this study adopts a model based on the coupling of two-dimensional hydrodynamics and one-dimensional pipeline networks to accurately simulate urban stormwater processes and calculate the total amount of surface water accumulation. Subsequently, the orthogonal experiment method is used to formulate an optimal operation scheme for storage tanks in the region, aiming at minimizing the total amount of surface water accumulation. Then the proposed model is applied to the case study of Xiaozhai area of Xi’an City, adopting design rainfall with the frequencies of 30, 50, and 100 years for the study of the optimal operation scheme for the storage tanks in this area. The results showed that the optimized operation rules of the storage tanks increased the total reduction rate of surface water accumulation by 12.93%, 8.72%, and 9.74% under different design rainfall scenarios, indicating that the storage tanks can provide better comprehensive benefits of flood control and drainage under the optimized operation rules. Storage tanks have a better optimization and reduction effect on rainfall with a smaller return period, but the optimization scheme still needs further research due to certain limitations of orthogonal experiments.