With the rapid development of urban metro system, the operation and maintenance status of urban metro station has received increasing attention. The operation and maintenance status of urban subway stations involve various factors including structure, equipment, and environment, which are difficult to be accurately evaluated directly. On the other hand, as the burial depth of metro station increases, disaster-triggering factors become increasingly complex and diverse, which enhances the difficulty of evaluating the operation and maintenance status. A new method is proposed herein to realize the comprehensive evaluation of the operation and maintenance status of urban deep metro stations. Firstly, the evaluation indexes needed for evaluation are selected by referring to a large number of literatures, combined with many relevant specifications and standards, and based on some existing index selection principles. According to the selected indexes, an evaluation index system of operation and maintenance status of underground metro station is established. Then, based on the established evaluation index system, a comprehensive evaluation method for the operation and maintenance status of urban deep metro station is developed by combining the analytic hierarchy process (AHP) and relevant information aggregation methods. This method is characterized by considering the functions with prominent defects with the use of weighted geometric average (WGA) and variable weight methods. Finally, the proposed evaluation scheme is applied to guide the maintenance of China’s deepest metro station. The proposed comprehensive evaluation method will promote the in-time management and maintenance of urban deep metro station.