It is valuable to study the spatiotemporal pattern of Japanese encephalitis (JE) and its association with the contextual risk factors in southwest China, which is the most endemic area in China. Using data from 2004 to 2009, we applied GISmapping and spatial autocorrelation analysis to analyze reported incidence data of JE in 438 counties in southwest China, finding that JE cases were not randomly distributed, and a Bayesian hierarchical spatiotemporal model identified the east part of southwest China as a high risk area. Meanwhile, the Bayesian hierarchical spatial model in 2006 demonstrated a statistically significant association between JE and the agricultural and climatic variables, including the proportion of rural population, the pig-to-human ratio, the monthly precipitation and the monthly mean minimum and maximum temperatures. Particular emphasis was placed on the time-lagged effect for climatic factors. The regression method and the Spearman correlation analysis both identified a two-month lag for the precipitation, while the regression method found a one-month lag for temperature. The results show that the high risk area in the east part of southwest China may be connected to the agricultural and climatic factors. The routine surveillance and the allocation of health resources should be given more attention in this area. Moreover, the meteorological variables might be considered as possible predictors of JE in southwest China.