The invention discloses a permanent magnet synchronous motor control method based on encoder automatic zero set. An improved high-frequency voltage injection method is used for detecting the initial position of a rotor, the initial position of the rotor is clear, voltage vectors can be applied conveniently, and a motor rotor reverse rotating phenomenon is avoided. Meanwhile, encoder zero compensation is carried out automatically, a compensation value is stored, direct calling in the future is convenient, and trouble of manual zero set is removed. Once calibration or zero reset is needed, operation through the method is carried out for one time, an encoder is subjected to accurate zero set again, a process is simple, and accuracy is high. The invention further discloses a control system which achieves the control method. After the initial position of the rotor is obtained through a rotor locating module, a voltage vector closest to the position is chosen to be applied, so that a rotor back-and-forth vibration phenomenon during locating is avoided, a high-frequency voltage signal is injected only before the rotor is located initially, phase lag and time lag cannot be brought to system operation, and noise cannot be introduced during operation.