Hydrological methods are commonly adopted in the simulation process of the optimization design of LID facilities, which is often flawed by low simulation accuracy. Here, an automatic optimization method for cost-benefit schemes of LID facility optimization design is proposed based on the NSGA-Ⅱ algorithm and high-precision urban one- and two-dimensional coupled hydrodynamic numerical model. Then, this method is applied to the optimization design of the sponge city construction in Xixian New District of Xi’an City, and three different construction cost schemes of the individual and combined LID facilities are analyzed respectively. The results show that the construction effects of the individual facility and combined LID facilities increase with the increase of the construction cost. In the same low-cost construction scheme, the construction effect of the combined LID facilities is lower than that of an individual LID facility, but as the construction cost continues to increase, the final construction effect of the combined LID facilities keeps increasing and then exceeds that of the individual facility. Using this method, decision makers can grasp the interaction between the cost and effect of the construction and choose an optimal scheme for the construction of LID facilities that meets actual engineering needs.