This study adopts rainwater harvesting systems (RWHS) into a stormwater runoff management model (SWMM) for the spatial design of capacities and quantities of rain barrel for urban flood mitigation. A simulation-optimization model is proposed for effectively identifying the optimal design. First of all, we particularly classified the characteristic zonal subregions for spatial design by using fuzzy C-means clustering with the investigated data of urban roof, land use and drainage system. In the simulation method, a series of regular spatial arrangements specification are designed by using statistical quartiles analysis for rooftop area and rainfall frequency analysis; accordingly, the corresponding reduced flooding circumstances can be simulated by SWMM. Moreover, the most effective solution for the simulation method is identified from the calculated net benefit, which is equivalent to the subtraction of the facility cost from the decreased inundation loss. It serves as the initially identified solution for the optimization model. In the optimization method, backpropagation neural network (BPNN) are first applied for developing a water level simulation model of urban drainage systems to substitute for SWMM to conform to newly considered interdisciplinary multi-objective optimization model, and a tabu search-based algorithm is used with the embedded BPNN-based SWMM to optimize the planning solution. The developed method is applied to the Zhong-He District, Taiwan. Results demonstrate that the application of tabu search and the BPNN-based simulation model into the optimization model can effectively, accurately and fast search optimal design considering economic net benefit. Furthermore, the optimized spatial rain barrel design could reduce 72% of inundation losses according to the simulated flood events.