Objective：A visual analysis system based on R Shiny was designed to analyze the prevalence of notifiable infectious diseases from 2004 to 2017，providing reference for disease control and prevention. Methods：Using R shiny and a variety of R packages，distribution was described and the visualized system was built based on four perspectives：population，time，space，and spatial-temporal interaction. Results：This system depicted spatial-temporal distribution maps of 39 notifiable diseases from 2004 to 2017，as well as disease clustering and age stratified heat maps. Meanwhile，it also performed time series analysis and spatial autoregression analysis on various notifiable infectious diseases. Conclusion：The R shiny visual analysis system has many advantages including simple operation and diverse analysis methods compared to other similar systems. And it is helpful to describe the epidemic characteristics of infectious diseases and facilitate the research of public health.