For the operational efficiency improvement of trains in railway transportation, Autonomous Train Control System (ATCS) is getting widespread research attention. The station is a main scenario for the autonomous train operation, and its passing capacity is one of the critical factors affecting the further release of line capacity potential for railway lines. Based on this, the paper proposes an autonomous route management system to enhance the efficiency of route management in stations. As a safety critical system, the functional safety and performance analysis of the system must be evaluated before it is implemented in practical application. Hence, Colored Petri Nets (CPNs) are used to formalize and evaluate the system. Afterward, based on the proposed CPNs models, functional safety is carried out by dynamic attribute analysis and computational tree logic. Moreover, considering the impact of communication delays and processing delays on the route resource allocation, a performance analysis of the autonomous route process for trains at the station is implemented through practical parameterizations. The results indicated that the proposed autonomous route management strategy can reduce the train operating time and train arrival interval in stations by 15.63 s and 24.9 s, respectively.