The construction of sponge cities in mountainous areas is crucial to achieving high-quality development in these regions. Owing to rugged terrain, significant changes in elevation, and uneven distribution of cities, the construction of sponge cities in mountainous areas faces challenges such as difficulties in clearing mountains and roads, high cost, and varying regional development requirements. However, there is currently limited research focusing on the impact of terrain on sponge city construction plans. In this study, we developed an optimal low impact development (LID) system layout method based on the annual runoff control rate. This study suggests implementing LID plans in stages to balance cost-effectiveness and enhance resilience. The optimized case1_100 scheme, which takes regional differences into account, can effectively achieve a runoff control coefficient of less than 0.25 in 98.86% of the area. Remarkably, this achievement comes at a significantly lower total cost of only 1.22 billion RMB compared to the unoptimized case2_100 scheme (which does not consider regional differences) with a cost of 3.03 billion RMB. Interestingly, the optimized case1_100 plan, selected using the Technique for Order of Preference by Similarity to Ideal Solution (TOPSIS) method, has an LID layout that is closely related to the surface terrain. Structural equation modeling analysis indicates that terrain affects land types, which in turn impacts the surface impermeability and runoff coefficients, ultimately influencing the corresponding LID deployment plan. The coefficients of relative elevation and slope on the final plan are determined as −0.13 and −0.77, respectively, with a high overall explanatory power of 0.84. This indicates that terrain characteristics have a significant impact on the spatial patterns and surface features of typical mountainous cities in China and the optimal LID strategy largely depends on the initial terrain conditions. This study provides valuable insights for optimizing LID construction in sponge cities, particularly in the context of new mountainous urban planning.