The invention discloses a ship-borne unmanned helicopter harpoon system, comprising a harpoon controller, an anchoring fork, a retraction actuating cylinder and a body connecting device, wherein the retraction actuating cylinder is mounted at the bottom of an unmanned helicopter through the body connecting device, the anchoring fork is connected with the bottom end of the retraction actuating cylinder, and the anchoring fork and the retraction actuating cylinder are driven and controlled by the harpoon controller. The ship-borne unmanned helicopter harpoon system has the advantages of simple structure, light weight, obvious locking effect and easy loading and unloading on the helicopter or on a deck; in comparison to pneumatic drive and hydraulic drive, the system designed by the invention needs not additionally matched weight-increasing devices such as a pneumatic supply and a hydraulic system in the body, and a driving power supply can directly use an on-board power supply, thereby greatly reducing the total weight; and the ship-borne unmanned helicopter harpoon system has the advantages of high precision, high environmental protection level, low noise and the like.