The invention discloses a beam-hopping synchronization method and system for multi-gateway stations oriented to high-throughput satellites. First, the ground gateway station group mainly includes a network control center, a master gateway station and a plurality of slave gateway stations, each gateway station generates service signals and synchronous control signals. Then, the forward link repeater in the beam hopping satellite payload separates the service signal and control signal sent by each gateway station, wherein the service signal is sent to the back-end power amplification link, and the synchronization control signal is sent to the beam hopping controller. For processing, the beam hopping controller analyzes and compares the synchronization control signals of multiple gateway stations, extracts the time error between the slave gateway station and the master gateway station, and at the same time, according to the analyzed beam hopping control instructions, the beam hopping The back-end switch link is controlled. The method has simple beam hopping synchronization process, fast synchronization time, simple and reliable on-board processing, and does not depend on a specific service communication system.