The present invention discloses a complex water area target tracking method based on an AIS (automatic identification system) and an active camera. The method comprises the following steps that: 1) an observation area is divided into n cells, each camera of an active camera group is separately calibrated according to each cell, so that the intrinsic parameters and extrinsic parameters of the cameras are obtained; (2) the AIS device is utilized to calibrate the cells in advance, and calibration information is stored, after a target object enters a relevant cell, the cell where the target object is located is determined according to position information returned by the AIS; (3) the active camera group is made to rapidly move to the area of the cell where the target is located, wherein the active camera group contains m active cameras; and (4) the clear video image of the target object is shot, and the target object is tracked according to an tracking algorithm. According to the method of the invention, a new image pickup idea is provided; and the cell division mode is adopted, and the AIS system and the cells are combined to determine the position and heading of the target object.