The invention discloses an anchor moored positioning system and an anchor moored positioning method for a deep stirring vessel. The anchor moored positioning system for the deep stirring vessel comprises a controller, a positioning system, six anchors, six anchor winches and a control handle, wherein the positioning system is used for measuring position and direction of the vessel and comprises aland measuring base station and two vessel-loaded movable stations; the anchors are connected to the vessel body through cable ropes and the cable ropes are provided with tensiometers; the anchors areused for reeling and unreeling the cable ropes, correspond to the anchors one by one, and are provided with braking systems and encoders; the control handle is used for controlling the anchor winchesto reel and unreel the cable ropes manually; and the positioning system, the anchor winches and the control handle are in signal connection to the controller. The position and direction of the deep stirring vessel can be controlled precisely by means of the positioning system. The position control precision of the deep stirring vessel can reach within +/-0.1 m, and the direction control precisionof the vessel can reach within +/-0.1 degree.