Objective To understand the report incidence rates of related communicable diseases in flood disaster areas,and discuss the effects of flood disaster on the incidence of communicable diseases. Methods The surveillance data of communicable disease in flood disaster areas (contain 69 counties) and non-disaster areas (contain 36 counties) in 2016 was collected, meanwhile collect the surveillance data from the same areas in 2015 and 2017. The situation of medical treatment in temporary shelter medical centers, living condition, drinking water and diet, implementation of disinfection and insecticidal measures were investigated in flood disaster areas. The Pearson chi-square tests were used to compare the report incidence rate of 11 kinds of flood disaster related diseases in the period of disaster versus pre-disaster and post-disaster. Results The report incidence rate of flood disaster related diseases in disaster areas was 74.77 per 100 000, while in non-disaster areas it was 76.04 per 100 000, there was 1.67% lower in disaster areas than non- disaster areas. Compared with pre-disaster and post-disaster, the report incidence rate was lower during the disaster period. Compared with 2015 and 2017, the report incidence rate was lower in 2016. In the post-disaster period, the report incidence rate in 2016 was 5.74% higher than in 2015 and 21.97% lower than in 2017, while in non-disaster areas it was both higher in 2016 than in 2015 and in 2017. There were no significant difference of the report incidence rate of hepatitis A and hepatitis E between disaster areas and non-disaster areas. A total of 8 public health emergencies among the 11 kinds of flood disaster related diseases were reported in 2016, while it was 9 and 52 in 2015 and in 2017, respectively. The public health emergencies reported during disaster and post-disaster in 2016 were less than in 2015 and in 2017. Conclusion The incidence of related communicable diseases is relatively stable the during the flood disaster period in 2016 in Anhui province. It achieved the goal of preventing major post-disaster epidemics.