The invention relates to a phase loss fault tolerant control method for a non-ideal sinusoidal counter electromotive force permanent magnet synchronous motor, which is characterized in that the unit counter electromotive force in a synchronous rotating coordinate system is obtained through performing coordinate transformation on an offline collected three-phase counter electromotive force of the permanent magnet synchronous motor, and the reference q-axis given current corresponding to the unit torque is derived according to the unit counter electromotive force and an electromagnetic torque formula under the synchronous rotating coordinate system. When a single-phase armature winding of the motor is disconnected, an equivalent relationship between the non-fault phase compensation current and a zero-axis compensation current reference value is obtained according to a principle that the electromagnetic torque of the motor is constant under normal and phase loss conditions, the torque ripple caused by the phase loss fault is compensated by adopting zero-axis voltage feedforward and current closed-loop compensation, and fault tolerant control for the non-ideal sinusoidal counter electromotive force permanent magnet synchronous motor under the phase loss fault is realized.