Models for the assessment of ecosystem services are important tools for policy-makers and researchers. However, the simulation results of different models vary greatly, and it is difficult for policy-maker to select a suitable model for specific areas. As a result, we compared the results of three hydrological ecosystem services (HESs) in a basin with diverse topography, Nansihu Lake basin, China, including the water supply, soil conservation and water purification services estimated by the Soil and Water Assessment Tool (SWAT) and the Integrated Valuation of Ecosystem Services and Tradeoffs (InVEST) model. Further comparisons of the HES results were conducted in the application of spatial pattern, priority and trade-off analyses through spatial statistics, hot spot and correlation analyses. Firstly, the results showed that the HES values in whole basin simulated by SWAT model were a little higher than those in InVEST model. Secondly, the spatial patterns of soil conservation service simulated by the two models were approximately similar in whole basin because of proximate simulation algorithm and input data, but the spatial distribution of the other two HESs varied greatly. In particular, the spatial patterns of water supply service simulated by the two models were more similar in hill areas than those in plain areas, while the spatial patterns of water purification service displayed opposite result. Furthermore, the distributions of hot and cold spots of HESs simulated by the two models were approximately consistent. Thirdly, the results of relation analysis to HESs were similar to SWAT and InVEST model roughly. The study suggested that the results of the two models could provide similar frames of reference for management and policy-making although different simulation results between the two models. This research can provide the theoretical basis for model selection, policy decision-making and regional ecosystem management.