This study conducts a life cycle environmental and economic quantification comparison of urban runoff source control facilities (URSCFs) through construction and operation stages in two urban functional regions (i.e., residential area and campus). From the environmental perspective, URSCFs construction in residential area has both higher environmental impacts and benefits than that in campus. The operation stage of URSCFs can observe significant benefit for both residential area and campus. We then develop a set of monetized method to make a comprehensive benefit evaluation (i.e., environmental, economic, and social benefit) of URSCFs. Overall, the two areas have payback time less than thirteen years for their investment which is acceptable when compared with the assumed total service period (30 years). Specifically, the payback time of campus is 5.62 years and residential area is 12.44 years. This implies that the campus has great potential to achieve high cost-benefit ratio and thus the Sponge City construction in campus can implement URSCFs with less engineering and material consumption due to its more spacious site than residential area with high building density. For both residential area and campus, permeable pavement has the highest environmental impact and economic cost because of the concrete consumption. Thus, we recommend that it should be cautious of the construction of concrete permeable pavement and find environmentally and economically alternatives in future URSCFs projects.