Urbanization significantly influences the capacity of ecosystems to provide services for humans. A better understanding of the response of ecosystem service capacity (ESC) to urbanization is essential for sustainable urban planning. The purpose of this study is to analyze the spatio-temporal patterns of ESC change during rapid urbanization in the Pingshan River Catchment in Shenzhen, China. We developed a multifactor analysis approach that links urban planning decisions to the ESC by integrating policy intervention-related variables, i.e., anthropogenic pressures and the typology, size, and spatial distribution of ecosystem service suppliers. Built-up areas and transportation systems associated with urbanization were two factors determining the interference intensity of anthropogenic pressures. The main ecosystem service suppliers were ecological lands involved in urban planning, including water bodies, forest lands, and grass lands. We performed a multifactor-based spatial superposition analysis in a geographic information system to produce spatio-temporal distribution maps of the ESC. Results revealed that with urbanization in 1990–2018, the ESC experienced a fluctuating downward trend before witnessing an upward trend. Areas with moderate ESC and above reduced from 63.3 % of the catchment area to 2.9 % in 1990–2015, and then increased to 21.3 % in 2018. This pattern of ESC change was mainly attributed to the extensive urban development since 1990, together with a series of environmental protection policy initiatives formulated since 2005. In terms of spatial distribution, the areas with moderate ESC and above dramatically reduced by 66.3 % during the study period and were predominantly located within ecological control zones by 2018. Based on the current status of the ESC, our findings can be beneficial to identify and prioritize urban intervention strategies, including land conservation, restoration, enhancement, retirement, and low-impact development. The proposed approach can also be applied to ESC evaluation and sustainable urban development of other urban regions.