Objective This paper was intended to analyze the spatiotemporal patterns of the Japanese encephalitis (JE) in Henan province from 2006 to 2010, and explore the connection between JE incidence and the geographical environmental driving factors. Methods The JE incidence from 2006 to 2010 in Henan was analyzed with epidemiological research, spatial autocorrelation, and correlation method. The multiple linear regression model was also built to identify the impact of meteorological, surficial and socio-economic factors on JE. Results The total number of JE case is 2 729 with yearly incidence of 0.547 4 per 100 thousand people and the overall death case was 119 with mortality rate of 4.36%. The incidence outbreak from July to September, accounting for 97.08% of the whole year cases and the annual incidence declined in 2008 and then fluctuated until 2010. JE cases were mainly concentrated in the southwest area, and "hot spots" agglomeration was significant in Luoyang, Nanyang, and northern Xinyang city. In terms of the meteorological driving factors, rainfall, the number of rainy days, >80% humidity days and >25℃ cumulated temperature promoted the outbreak of JE, while >30℃ cumulated days and the maximum above 30℃ cumulated temperature would reduce the incidence. For the surficial factors, watershed density and cultivated area illustrated the significant correlation with incidence of 99% confidence. With the increase of income per capita in farmers and total number of health technical staff, the possibility of an outbreak of JE also decreased. The overall predicted R² of regression model was 0.643 with the adjusted R² of 0.414. Conclusion The southwest area in Henan province is the key area for JE management. Research on the geographical driving factors of JE disease, will have a significant effect on the prevention and control of JE incidence.