Hand, foot and mouth disease (HFMD) is a common infectious disease, causing thousands of deaths among children in China over the past two decades. Environmental risk factors such as meteorological factors, population factors and economic factors may affect the incidence of HFMD. In the current paper, we used a novel model-geographical detector technique to analyze the effect of these factors on the incidence of HFMD in China. We collected HFMD cases from 2,309 counties during May 2008 in China. The monthly cumulative incidence of HFMD was calculated for children aged 0-9 years. Potential risk factors included meteorological factors, economic factors, and population density factors. Four geographical detectors (risk detector, factor detector, ecological detector, and interaction detector) were used to analyze the effects of some potential risk factors on the incidence of HFMD in China. We found that tertiary industry and children exert more influence than first industry and middle school students on the incidence of HFMD. The interactive effect of any two risk factors increases the hazard for HFMD transmission.