Objective: To analyze the relationship between the incidence of bacterial dysentery and related meteorological, environmental and socio-economic factors in parts of southwest China, under the geodetector. Methods: Incidence data on bacillary dysentery from 2005 to 2014 was collected from the China infectious disease reporting system and meteorological, terrain environment and socio-economic related data were used for statistical analysis with geodetector also used, in Sichuan province, Yunnan province and the Tibet autonomous region (southwest China). Results: Through geodetector model, results showed that the elevation maximum value of power of determinant (PD) (PD=0.308), ethnicity (PD=0.260), followed by summer mean temperature, topography, elevation standard deviation, slope, population density were noticed. The maximum value of PD of summer average relative humidity, summer average precipitation, and regional GDP were all less than 0.200. In the ecological detector model, value of PD appeared significantly different from multiple factors such as summer average precipitation, regional GDP, average altitude, elevation standard deviation, slope, terrain and ethnicity (P<0.05). In the interactive detector model, after the spatial interaction, factors as: value on PD of summer average relative humidity, population density and regional GDP were larger than the value on the sum of PD of two factors with nonlinear superposition enhancing trend. Results from the risk zone detection showed that areas of moderate average summer temperature, low average precipitation, moderate average summer relative humidity, high average altitude, large elevation standard deviation, high slope, mountain topography, Tibeto-Burmese of ethnicity, low population density, low regional GDP were all related to the high incidence rates of bacterial dysentery. Conclusions Meteorological conditions and topography environments were related to the bacterial dysentery in southwest China, socio-economic behaviors depends on the level of economic development and sanitary conditions etc. were all directing influencing the transmission and incidence of bacterial dysentery. For developing a better intervention programs on bacillary dysentery, socio-economic means should be used for the control of bacillary dysentery, in the region.