Abstract: Application of muscle synergy theory to upper limb rehabilitation after stroke is expected to provide new technology and guiding strategies for standardized assessment and intervention in clinical rehabilitation. For the human motion modular control strategy based on muscle synergy theory, the mathematical model and characteristics of muscle synergy are summarized. The research status of muscle synergy in upper limb rehabilitation after stroke in recent years is analyzed, including motor injury assessment, rehabilitation effectiveness evaluation, rehabilitation intervention guidance, and effectiveness evaluation of rehabilitation robots. Then the potential challenges to the muscle synergy development are discussed. Finally, the research progresses of muscle synergy theory in clinical rehabilitation applications are summarized and the development trends are prospected.