The invention provides a hybrid crop transgenic safety control method. An transgenic plant automatic deletion double-unit system, comprising a recombinase system, a transcription activation system and an exogenous gene expression control system, is established; and a plant flower primordium cell specific promoter is utilized as a promoter in the transgenic plant automatic deletion double-unit system to control the transcription activation system, and the transcription activation system controls the start of the recombinase system, so that the exogenous gene introduced into the plant stably exists in the F1-generation plant hybrid as well as root, stem, leaf and other non-deletion tissues, but is deleted in the pollen and seed of the F1-generation plant, thereby implementing the hybrid crop transgenic safety control.