The invention provides a machining method for improving the machining quality of high-precision special-shaped long shaft parts. Through design of a process boss, the problem of poor part machining quality caused by imbalance during machining of special-shaped long shaft parts is solved, and the problem that a special-shaped shaft is hard to locate and clamp is improved. Through twice semi-finishing machining, the problems that the high-precision special-shaped long shaft parts are large in machining allowance, prone to machining deformation and hard to control are solved. During finishing machining, the special-shaped shaft is subjected to segmented machining in a machining allowance progressive decreasing mode, and the problems that the high-precision special-shaped long shaft parts havethe high precision requirement and are poor in structure rigidity and machining quality are solved. Through the three-time heat treatment process, machining stress is fully released, and deformationof the parts is reduced. Deformation of the parts is reduced through the twice heat treatment destressing mode. The machining efficiency is improved. The machining precision is ensured. The productivity is improved. The machining cost is lowered.