This paper presents a super efficiency network Data Envelopment Analysis (SE-NDEA) model for eleven cities in China. The model focuses on measuring the performance of public transit system by integrating multiple stakeholders involved in public transit system with the exogenous environment in where they operated. Thus, local authority, bus operators, passengers, uncontrollable environmental factors, and the externality of public transit are all taken into account in the measurement framework. They are interrelated inputs and outputs. The measurement framework can simultaneously capture each public transit system’s production efficiency, service effectiveness, and operational effectiveness. Meanwhile, undesirable outputs, uncontrollable factors, and boundary-valued variables are considered. The paper evaluates the performance of public transit system of 11 Chinese cities from 2009 to 2016. The results reveal that the exogenous environment has a marked impact on the performance measurement of public transit system. Super cities tend to perform better than mega cities, and mega cities tend to perform better than large cities. Furthermore, service effectiveness has a significantly positive correlation with production efficiency, and transit rail tends to perform better than the conventional bus. These findings have an important implication for China’s bus priority implement and more general managerial insights for public transit development.