Sponge city is a national sustainable stormwater management program proposed by the Chinese government to deal with urban water issues (e.g., flooding, poor water quality) brought on by climate change and urbanization. Various strategies for sponge city construction are required since environmental constraints differ regionally across the country. To identify regional variations, reveal the inner links between externalities and design elements in sponge city construction, and offer practical suggestions, efforts in two directions are made based on the data of 68 sponge city cases around China: 1) discussing design parameters of four Low Impact Development (LID) facilities, including bioretention cell, permeable pavement, grass swale, and sunken green space, under four regionalization maps of hydrologic, climatic, landform and soil texture factors, and 2) building a holistic Partial Least Squares-Structural Equation Modelling (PLS-SEM) model illustrating the relationship between local characteristics, LID system design, and LID system performance in sponge city construction. The results show that: 1) rainfall and landform factors have great impact on LID facilities design, as their depths tend to be higher in water rich areas and coastal areas. 2) LID types and areas are positively influenced (+0.745) by the total area and permeable portion of a project, while the LID system performance (water quantity and quality control) is negatively impacted (−0.407) by the rainfall amount and clay fraction. 3) comprehensive LIDs choice instead of single LID facility shows more significant effect on improving LID system performance. It is recommended to establish different design standards and assessment indexing systems tailored to local environment when constructing sponge city projects.