The invention provides a spatial alternation based train control system movement authority safety protection method. The method mainly comprises the steps that train control system rail sections and a spatial alternation expression method for elements included in the sections are established, and a spatial alternation algorithm for movement authority safety protection is established based on the spatial alternation expression method; based on a target terminal point distance in train movement authority, a train safety protection curve is generated, and a train trajectory calculating method is established according to the train safety protection curve; according to the spatial alternation algorithm for movement authority safety protection, protection verification is conducted on train trajectories and train movement authority, and the safety of the train trajectories and train movement authority is determined according to verification results. The method can effectively conduct safety verification on generated MA information and train trajectories, the safety of MA is ensured, and the train operating safety is guaranteed.