Stormwater runoff is a major concern in urban areas which is mostly the result of vast urbanization. To reduce urban stormwater runoff and improve water quality, low impact development (LID) is used in urban areas. Therefore, it is vital to find the optimal combination of LID controls to achieve maximum reduction in both stormwater runoff and pollutants with optimal cost. In this study, a simulation–optimization model was developed by linking the EPA Storm Water Management Model (SWMM) to the Multi-Objective Particle Swarm Optimization (MOPSO) using MATLAB. The coupled model could carry out multi-objective optimization (MOO) and find potential solutions to the optimization objectives using the SWMM simulation model outputs. The SWMM model was developed using data from the BUNUS catchment in Kuala Lumpur, Malaysia. The total suspended solids (TSS) and total nitrogen (TN) were selected as pollutants to be used in the simulation model. Vegetated swale and rain garden were selected as LID controls for the study area. The LID controls were assigned to the model using the catchment characteristics. The target objectives were to minimize peak stormwater runoff, TSS, and TN with the minimum number of LID controls applications. The LID combination scenarios were also tested in SWMM to identify the best LID types and combination to achieve maximum reduction in both peak runoff and pollutants. This study found that the peak runoff, TSS, and TN were reduced by 13%, 38%, and 24%, respectively. The optimal number of LID controls that could be used at the BUNUS catchment area was also found to be 25.