Current centralized urban water supply depends largely on energy consumption, creating critical water-energy challenge especially for many rapid growing Asian cities. In this context, harvesting rooftop rainwater for non-potable use has enormous potential to ease the worsening water-energy issue. For this, we propose a geographic information system (GIS)-simulation-based design system (GSBDS) to explore how rainwater harvesting systems (RWHSs) can be systematically and cost-effectively designed as an innovative water-energy conservation scheme on a city scale. This GSBDS integrated a rainfall data base, water balance model, spatial technologies, energy-saving investigation, and economic feasibility analysis based on a case study of eight communities in the Taipei metropolitan area, Taiwan. Addressing both the temporal and spatial variations in rainfall, the GSBDS enhanced the broad application of RWHS evaluations. The results indicate that the scheme is feasible based on the optimal design when both water and energy-savings are evaluated. RWHSs were observed to be cost-effective and facilitated 21.6% domestic water-use savings, and 138.6 (kWh/year-family) energy-savings. Furthermore, the cost of per unit-energy-saving is lower than that from solar PV systems in 85% of the RWHS settings. Hence, RWHSs not only enable water-savings, but are also an alternative renewable energy-saving approach that can address the water-energy dilemma caused by rapid urbanization.