The invention discloses a method and a system for train start-up mark alignment according to a transponder number, which can realize start-up mark alignment in a section, has a simple and direct realization mode, does not need to add other external equipment as a premise, and solves the problem that the section cannot start-up mark alignment and the risk of not calling a data-controlled vehicle. The technical scheme is as follows: the invention inputs the number of the transponder by the driver, determines the automatic calibration position by matching the transponder information, realizes thetrain monitoring and recording device to accurately organize the data to control the train, improves the accuracy of the data of the control car, and also improves the efficiency of the railway transportation.