Extreme rainfalls could greatly affect operations of urban rail transit systems of mountainous cities, which are prone to have landslides and floods under rainfalls. Therefore, it is essential to assess and enhance the resilience of mountainous urban rail transit networks under heavy rainfalls. Taking the metro network of Chongqing, the largest mountainous city in China, as an example, this study establishes a network topology model to identify the high-risk nodes under rainfalls and find the effective recovery strategies. By introducing the metro ridership and topological shortest distances, a network service efficiency function is developed, and the importance of nodes is quantified using service efficiency index and topological importance index. The resilience assessment model based on service efficiency is constructed using the resilience triangle theory. Additionally, risk levels for landslide and flood-prone areas are classified using the K-means algorithm, based on rainfall, elevation, and slope data, identifying high-risk stations. Finally, the node recovery sequence and strategies for high-risk nodes affected by landslides and floods are examined. The results indicate that in extreme rainfall scenarios, two transfer stations (Daping and Fuhua Road) are among the high-risk landslide stations, while most other nodes have a service efficiency index of less than 0.2. High-risk flood stations are located on non-transfer lines and mostly on metro lines with high traffic flow, with service efficiency index generally high, with some stations, like Bijin Station, exceeding 0.3. When all affected nodes fail, network service efficiency decreases by 84.0% and 75.2% under landslide and flood disasters, respectively. Compared with the random recovery strategy, recovery strategies based on topological importance and service efficiency index, the optimal recovery strategy based on genetic algorithm performs much better.