Disclosed are an auxiliary disassembling and assembling tooling for a ship propeller shaft and the application thereof, the tooling comprising: a flatcar (1); a conveying device (2) mounted on an upper surface of the flatcar (1); a supporting device mounted on the conveying device (2) and used for supporting a propeller shaft (100), the supporting device comprising several height-adjustable supporting portions (3) arranged side-by-side at intervals; and a controller in connection with the conveying device (2) and used to control the action of the conveying device (2), so as to push the supporting device to move in the lengthwise direction of the flatcar (1). When the propeller shaft is disassembled and assembled with the above tooling, it is not necessary to make a propeller shaft mounting jig frame, thus reducing the cost of disassembling and assembling the propeller shaft, and also being able to quickly disassemble and assemble the propeller shaft, and improving the disassembling and assembling efficiency and installation accuracy of the propeller shaft.