The invention relates to a capture method and system for train virtual transponders. The method for the train virtual transponder comprises the steps that the running direction of a train is determined, the capture zones of the virtual transponders on a train running rout are determined, and the capture state of the current virtual transponders is judged; if the current virtual transponder is in the capture missing state, the first calculation capture time is calculated according to the train current positioning time and the train running state, and the first calculation capture time is the capture time of the current virtual transponders. According to the capture method and system, the virtual transponder in the capture missing state is recorded, the capture time of the virtual transponder in the capture missing state is reckoned through the train positioning position and the virtual transponders in the capture state, the capture accuracy and the capture probability of the virtual transponders on the train running rout are improved, and it is ensured that the train runs safely and reliably.