Rail transit stations with multifloor structures have been built in many cities to intensively utilize land resources and facilitate lives of community. However, being overcrowded with passengers results in high risks during daily operation. In response, this study conducted an emergency evacuation simulation and optimization in the three-dimensional (3D) space of “complex rail transit stations” (CRTSs). The aim of the paper is to provide a methodology to determine effective emergency evacuation strategies for CRTSs. The Lianglukou Rail Transit Station in Chongqing, China, was used as a case study and the AnyLogic simulation platform employed for simulating emergency evacuations. An emergency evacuation theoretical framework was established. The emergency evacuation strategies, including evacuation routes and evacuation times, were determined based on the theoretical demonstration. Simulation and optimization of emergency evacuation in the Lianglukou station were conducted. Accordingly, four main simulation results were obtained: (1) Escalators/stairs and turnstiles are key facilities in the evacuation; (2) Effective guidance for the evacuation is necessary in the public space of the station; (3) Passenger aggregation nodes should be guided for balanced evacuation; (4) Removing metal barriers is a useful evacuation optimization measure. The proposed research method and framework can be used by other CRTSs in the establishment of emergency evacuation strategies and effective optimization strategies to promote safety of transportation system. The research findings are beneficial to passengers in helping them provide valuable emergency evacuation guidance.