The phase current of the permanent magnet synchronous motors (PMSM) commonly contains nonnegligible sideband harmonics due to the working characteristic and the pulse-width-modulation (PWM) of the power electronics for power supply, especially at high speed operation. These harmonics will degenerate the output performance of machine, generate additional losses, and threaten the thermal safety. Therefore, the current harmonics are eager to be accurately obtained and analyzed in real-time to achieve better status monitoring and diagnosis. This paper proposes a high-accuracy online estimation method for harmonics with good portability, which has been validated by the comparison of online/offline results. Moreover, obtaining the harmonic distribution and magnitudes can also provide a reliable reference for numerous future analysis and optimization in the motor design stage.