The invention discloses a space vector modulation based harmonic current compensation system for a high-speed permanent magnet motor. The system comprises a rotor position and speed observation module, a stator phase current harmonic compensation module, a phase current feedback module, a rotation speed PI adjustment module, a current PI adjustment module and an SVPWM (space vector pulse width modulation) conversion output module. The stator phase current harmonic compensation module comprises a harmonic current extraction module, a proportional controller, a harmonic current adjustment module and a harmonic voltage compensation amount calculation module. The harmonic current extraction module extracts phase current harmonics of a permanent magnet synchronous motor in real time by the aid of an adaptive band-pass filter; the proportional controller adjusts the harmonic current and feeds the harmonic current to a current loop; the harmonic current adjustment module and the harmonic voltage compensation amount calculation module are used for calculating harmonic voltage compensation amount on the basis of a mathematical model of the high-speed permanent magnet motor and feeding back to the voltage loop. By the space vector modulation based harmonic current compensation system for the high-speed permanent magnet motor, voltage compensation amount can be calculated accurately, real-time compensation can be realized, phase current waveforms in operation of the permanent magnet synchronous motor can be improved effectively, torques and rotation speed pulses can be reduced, and accordingly operation efficiency, stability and reliability of the motor can be improved.