The invention discloses a method for realizing a configurable secure communication protocol for a train control system based on communication. The train control system based on communication comprises an application layer and a hardware driving layer/security layer. The method comprises the following steps: setting a configurable secure communication protocol layer comprising a configurable secure communication protocol stack and a function interface between the application layer and the security layer, so that the application layer can configure the configurable secure communication protocol stack by calling the function interface to support various secure communication protocols for the communication between a plurality of components of the train control system. The configurable secure communication protocol comprises RSSP-I, RSSP-II and other secure communication protocols, a series of other security check modes is further provided at the same time, and a user can define different security check combinations in a configuration manner so as to a butt joint with the existing secure communication protocols of other subsystems without changing codes.