The epidemiology of schistosomiasis japonicum over small areas remains poorly understood, and this is particularly true in China. We aimed to identify high-risk areas for schistosomiasis and associated risk factors in the Poyang Lake region, China. A cross-sectional study was conducted and 60 of 920 persons (6·5%) were found to be infected with Schistosoma japonicum. Locations of households and snail habitats were determined using a hand-held global positioning system. We mapped the data in a geographical information system and used spatial scan statistics to explore clustering of infection, logistic regression and Bayesian geostatistical models to identify risk factors for each individual's infection status and multinomial logistic regression to identify risk factors for living in a cluster area. The risk of schistosomiasis was spatially clustered and higher in fishermen and males, not in persons who lived in close proximity to snail habitats and infected water sources. This study has demonstrated significant spatial variation in the prevalence of schistosomiasis at a small spatial scale. The results suggest that demographic factors (gender, occupation) rather than the distance to infected water are driving human transmission at small-scale spatial levels. Such information can be used to plan locally targeted interventions based on anthelminthic drug administration, snail control and sanitation improvement.