The invention provides a method for controlling heat treatment microdeformation of a wind power equipment gear main shaft. The method comprises the following steps: preheating a gear shaft, carburizing, cooling down, quenching, cleaning the gear shaft, and tempering. Processing parameters of heating temperature, heat preservation time, carburizing concentration, cooling speed, quenching oil temperature, burner gas, pressure and the like in the entire process are controlled. Through the adoption of the method, the problems of over large carburizing quenching deformation, inconsistent carburizing depths, big stress gradient and the like in the heat treatment process are solved, and a uniform and fine metallographic structure is obtained, so that a spline with high strength and high precision is obtained; the mechanical property is improved, the transmission quality is guaranteed, and the service life is prolonged.