Aiming at the frequent phenomenon of waterlogging in mountainous and hilly cities, taking a mountainous and hilly city in the southeast as an example, on the basis of evaluating the waterlogging risk and analyzing the current drainage and waterlogging prevention in the areas, based on the thinking of overall planning for flooding and waterlogging, the drainage and waterlogging prevention system of flooding control, waterlogging prevention and exceeding standard emergency in the basin is built from the perspective of river flooding prevention, mountain torrents drainage, source emission reduction, pipe network discharge, combination of storage and discharge, daily operation and maintenance management, exceeding standard emergency system. The simulation results show that the scheme can effectively eliminate the regional waterlogging and reduce the waterlogging risk after implemented.