The development of sponge cities advocates for sustainable urban rainwater management, effectively alleviating urban flood disasters, reducing non-point-source pollution, and promoting the recycling of rainwater resources. Low-Impact Development (LID) serves as a key strategy in this context, providing essential support for urban rainwater control and pollution reduction. To investigate the runoff control effects of LID measures and to reveal the relationship between facility runoff control performance and installation scale, this study focuses on a sponge community in Beijing. A SWMM model was constructed to analyze the rainwater flood control and pollutant load reduction effects of different LID facilities, including bio-retention cells, green roofs, and permeable pavements. Using evaluation indicators such as surface runoff, node overflow, and pollutant control rates, this study examined how facility performance varies with installation scale under different rainfall conditions. The combination scheme of LID equipment optimal configuration is designed by using multiple criteria decision analysis (MCDA) and cost–benefit theory. The results indicate significant differences in performance among the various LID facilities across different rainfall scenarios. Specifically, the optimal installation proportion for runoff and overflow control of permeable pavements were found to be between 30% and 70%. Green roofs demonstrate superior performance in handling extreme rainfall events, while bio-retention cells exhibit significant effectiveness in controlling Total Suspended Solids (TSSs). Through comprehensive performance evaluation, this study identified the optimal combination scale under a 3-year rainfall recurrence interval as 30% permeable pavements, 20% green roof, and 60% bio-retention cells. This combination effectively leverages the strengths of each facility, ensuring system stability and efficiency while also demonstrating optimal management efficiency in cost–benefit analyses. The findings of this research provide valuable insights for future urban water management and infrastructure development.