The invention discloses a method for prefabricating pipe joints of an immersed tube tunnel. The method comprises the following steps that 1, steel bars are bound in a shallow dry dock, and the pipe joints are poured; 2, a steel end shell, a steel end sealing wall and a guiding device are arranged at the two ends of each pipe joint; 3, a waterproof layer of each pipe joint is constructed; 4, prefabricated plates are prefabricated in a prefabricated site beside an assembling platform; 5, a dock door is opened, the pipe joints are conveyed to the assembling platform in a floating mode, and a hoisting system is arranged on the assembling platform; 6, the prefabricated plates are hoisted to the corresponding positions of the pipe joints through the hoisting system; 7, the waterproof layers areapplied above the prefabricated plates; and 8, the pipe joints are dragged to designated positions for reassembling and then sinking. According to the method, the pipe joint floating process is shallow in draft depth, the temporary project is little, the dredging amount in water or dredging is not needed, the environment influence is small, and streamlined operation can be carried out.