The purpose of this study is to evaluate the sustainable operation of rail transit system. In rail transit system, as the most important aspect of negative entropy flow, the effective strategy can offset the increasing entropy of the system and make it have the characteristics of dissipative structure, so as to realize the sustainable operation. At first, this study constructs the Pressure-State-Response (PSR) model to evaluate the sustainable operation of rail transit system. In this PSR model, “pressure” is viewed as customer requirements, which answers the reasons for such changes in rail transit system; “state” refers to the state and environment of system activities, which can be described as the challenges of coping with system pressure; “response” describes the system’s actions to address the challenges posed by customer needs, namely operational strategies. Moreover, then, 13 pressure indices, five state indices and 11 response indices are summarized. In addition, based on quality function deployment (QFD), with 13 pressure indices as input variables, five state indices as customer requirements (CRs) of QFD and 11 response indices as technical attributes (TAs) of QFD, this study proposed the three-phase evaluation method of the sustainable operation of rail transit system to obtain the operational strategy (that is, negative entropy flow): The first phase is to verify that 13 pressure indices can be clustered into five state indices by fuzzy clustering analysis; The second phase is to get the weights of five state indices by evidential reasoning; The third phase is to rate the importance of 11 response indices by integrating fuzzy weighted average and expected value operator. Finally, the proposed model and method of evaluation are applied to the empirical analysis of Shanghai rail transit system. Finally, we come to the conclusion that Shanghai rail transit system should take priority from the following five aspects: “advancement of design standards”, “reliability of subway facilities”, “completeness of operational rules”, “standardization of management operation” and “rationality of passenger flow control”.