With the aim of exploring the usefulness of spatial analysis in the formulation of a strategy for schistosomiasis japonica control in different environmental settings, a population-based database was established in Dangtu county, China. This database, containing the human prevalence of schistosomiasis at the village level from 2001 to 2004, was analyzed by directional trend analysis supported with ArcGIS 9.0 to select the optimum predictive approach. Based on the approach selected, different strata of prevalence were classified and the spatial distribution of human infection with Schistosoma japonicum was estimated. The second-order ordinary kriging approach of spatial analysis was found to be optimal for prediction of human prevalence of S. japonicum infection. The mean prediction error was close to 0 and the root-mean-square standardised error was close to 1. Starting with the different environmental settings for each stratum of transmission, four areas were classified according to human prevalence, and different strategies to control transmission of schistosomiasis were put forward. We conclude that the approach to use spatial analysis as a tool to predict the spatial distribution of human prevalence of S. japonicum infection improves the formulation of strategies for schistosomiasis control in different environmental settings at the county level.