To suppress the high-order current harmonic in five-phase permanent magnet synchronous machines (FPMSMs), the mathematical model of FPMSMs with high-order harmonics is proposed. Then, based on this model, the multiple synchronous rotating frame transformations (MSRFTs) algorithm of FPMSM is proposed to convert the 7th-order and 9th-order harmonics in the stationary coordinate system into the DC quantities in the 7th-order and 9th-order SRFs, respectively. In order to extract current harmonics accurately, this paper further designed a frequency adaptive low-pass filter to achieve good filtering effect in the full speed range of the motor. Simulation results show that the proposed algorithm can suppress the current harmonics effectively.