Aiming at the low harmonics caused by open winding permanent magnet synchronous motor (OW-PMSM) with the common DC bus, the adaptive notch filter (ANF) based on the least mean square (LMS) algorithm is adopted to control the 3rd, 5th, and 7th harmonics in the system. And, an ANF based on the LMS algorithm is used to suppress the 3rd, 5th and 7th harmonics in the system. Firstly, the mechanism of the low harmonics generation in the OW-PMSM is analyzed. Then, with the help of Matlab/Simulink, a 120° decoupling modulation strategy is explored to eliminate the zero-sequence currents caused by the modulation on the inverter side, and the ANF is used to extract the harmonics of the corresponding frequencies in the system, and the extracted harmonics are compensated into the current loop. More, the low harmonics caused by nonlinear factors are suppressed. Finally, the simulation and experimental results show that the contents of the 3rd, 5th, and 7th harmonics in the system are significantly reduced by adopting the ANF.