Precisely delineating the spatiotemporal heterogeneity of water conservation services function (WCF) holds paramount importance for watershed management. However, the existing assessment techniques exhibit common limitations, such as utilizing only multi-year average values for spatial changes and relying solely on the spatial average values for temporal changes. Moreover, traditional research does not encompass all WCF values at each time step and spatial grid, hindering quantitative analysis of spatial heterogeneity in WCF. This study addresses these limitations by utilizing an improved water balance model based on ecosystem type and soil type (ESM-WBM) and employing the EFAST and Sobol’ method for parameter sensitivity analysis. Furthermore, a space–time cube of WCF, constructed using remote-sensing data, is further explored by Emerging Hot Spot Analysis for the expression of WCF spatial heterogeneity. Additionally, this study investigates the impact of two core parameters: neighborhood distance and spatial relationship conceptualization type. The results reveal that (1) the ESM-WBM model demonstrates high sensitivity toward ecosystem types and soil data, facilitating the accurate assessment of the impacts of ecosystem and soil pattern alterations on WCF; (2) the EHSA categorizes WCF into 17 patterns, which in turn allows for adjustments to ecological compensation policies in related areas based on each pattern; and (3) neighborhood distance and the type of spatial relationships conceptualization significantly impacts the results of EHSA. In conclusion, this study offers references for analyzing the spatial heterogeneity of WCF, providing a theoretical foundation for regional water resource management and ecological restoration policies with tailored strategies.