The invention discloses a method for manufacturing buoyancy tanks of a semi-submerged ship, which comprises the following steps of: (1) marking the center line of a movable jig frame, an involution line, the lower bottom position line and the top position line of an upper buoyancy tank as well as the upper top position line and the lower bottom position line of the lower buoyancy tank by using a total station on a jig position, and controlling the position line distance between the lower bottom of the upper buoyancy tank and the upper top of the lower buoyancy tank to be between 1 mm and 4 mm; (2) respectively manufacturing six face sheets of the upper buoyancy tank and sixe face sheets of the lower buoyancy tank on a platform; (3) respectively suspending the respective six face sheets ofthe upper buoyancy tank and the lower buoyancy tank to build the buoyancy tanks; (4) completing the assembly and welding of limiting slide slots of the upper buoyancy tank and the lower buoyancy tank, and completing the matching and drilling of connecting bolt holes of the upper buoyancy tank and the lower buoyancy tank; and (5) respectively and vertically suspending the upper buoyancy tank and the lower buoyancy tank by using a crane to leave the movable jig frame after the upper buoyancy tank and the lower buoyancy tank are approved to be qualified, and completing the separation of the upper buoyancy tank and the lower buoyancy tank in the air. The invention not only ensures the high-precision building requirements of the upper buoyancy tank and the lower buoyancy tank, but also completes the matching and drilling works of the connecting bolts of the upper buoyancy tank and the lower buoyancy tank in a section in advance.