This paper aims to realize the extensive application of Internet of things technology in urban waterlogging prevention management system, and has analyzed the security requirement and security architecture of Internet of things technology, and discussed the demand of urban waterlogging prevention management system in combination with the key technology of Internet of things technology, to do the overall design and functional design well during designing of urban waterlogging prevention management system. Finally, the application process of the Internet of things technology in Chongqing waterlogging prevention management system is summarized. The application result shows that the flood control and drainage function of Chongqing is gradually improved with smooth drainage facilities;the inspection and maintenance management is gradually standardized;operation monitoring and early warning management is fully strengthened. There is visual management for emergency command and dispatch, and at the same time, the drainage pipe network assessment management can be conducted correctly.