Taking three kinds of municipal infrastructures, i.e. underpass, rail transit and tunnel as the research object, the waterlogging causes of municipal infrastructures in the mountainous cities are analyzed and summarized. Combined with the historical waterlogging situation in the central area of Chongqing and by applying the multiple risk analysis methods of field investigation and literature research, a three-level assessment method for the waterlogging prevention and control capacity of important municipal infrastructures in mountainous cities is constructed, which aims to quickly evaluate the waterlogging prevention and control capacity of municipal infrastructures in the low-lying areas and provide the technology and data supports for the subsequent waterlogging treatment work. For the high-risk facilities, the hydraulic model method is used to check the waterlogging risks. The medium-risk facilities are checked by the reasoning formula method, and the low-risk facilities cannot be checked.