Data mining in infectious disease pandemic scenarios is a complex giant task involving data from various fields and requirements of real-time and dynamic. In this paper, we propose a graph mining system for the infectious disease pandemic, IDGMS, with one-stop, dynamic, and interactive characteristics. The system has been applied to solve problems from three view scales and performs well. The system is constructed as a loose coupling structure at the front and back ends and can be extended to more graph mining issues. To the best of our knowledge, we are the first graph system especially targeting data mining of infectious diseases.