Abstract: Objective To investigate the spatial and temporal distribution of bacillary dysentery in the three gorges area from 2014 to 2016,and provide evidence for both further investigation of risk factors and interventions. Methods The incidence and outbreak data of bacillary dysentery in the three gorges area from 2014 to 2016 were obtained from National Notifiable Infectious Disease Reporting System and National Public Health Emergency Reporting Information System. The spatial autocorrelation analysis and spatial-temporal scan statistic were conducted by using software GeoDa1.8.16.4 and SaTScan 9.4 respectively. The results were visualized by using software ArcGIS 10.3. Results The reported annual incidences of bacillary dysentery in the three gorges area from 2014 to 2016 were 24.00/100 000,22.14/100 000 and 20.84/100 000 respectively,showing a decrease trend. Only 1 bacillary dysentery outbreak was reported in Chengkou county in the northeast of Chongqing and the attack rate was 5.36%(70/1 305). Global spatial autocorrelation indicated that there was a spatial clustering in the incidence of bacillary dysentery(In turn,Moran's I coefficient is 0.194,0.227,0.482,and P=0.001). Local spatial autocorrelation showed that the number of hot spot areas was 2,5 and 8 during 2014-2016 respectively. The number of cold spot areas had slight change,which was 6,6 and 8 during 2014-2016 respectively. Spatial-temporal scan statistic analysis found that the clustering period was during May-October in class Ⅰ cluster areas steadily found in southwest Chongqing,including Yuzhong,Dadukou,Jiangbei,Shapingba,Jiulongpo,Nanan,Beibei,Yubei, Banan districts and Changshou county. Bishan county was included in 2014 and 2015,and Hechuan district was included in 2016. A total of 4,3 and 5 class Ⅱ cluster areas were found from 2014 to 2016 respectively,including Chengkou county of Chongqing,Xiling and Wujiagang districts of central Yichang all the time. Conclusion The incidence of bacillary dysentery had spatial and temporal clustering at county level in the three gorges area,and the areas with high incidences were the urban area of Chongqing and its surrounding counties. Spatial statistical analysis is suitable for the analysis of the spatial and temporal clusters of bacillary dysentery and can provide useful information for the disease prevention and control in the future.