The reasonable risk evaluation in the long-term operation of urban subway systems is of importance to the public safety and maintenance work of the subway. At present, the risk assessment always depends on a specified single factor which might result in a biased risk result. In order to take more influential factors into account, the multiple indices system is developed for the total risk evaluation in this work. The proposed multiple indices system is established on the basis of the logical structure of the analytic hierarchy process (AHP). It is based on the 7 selected factors in which the value of each factor is defined by its risk level and the corresponding weight is determined by the AHP calculation. The result obtained from the case study showed that the total risk levelgot from the proposed method is more reasonable than the traditional single index-based methods.