With the advantages of high speed, low noise and high efficiency, the electromagnetic suspension (EMS) type maglev train has a good prospect in railway transportation. It is based on the long stator linear synchronous motor (LSLSM). However, due to cogging effect, end effect and the harmonics in the stator current and flux density distribution around the air-gap, the thrust generated by the LSLSM fluctuates. The thrust ripple brings noise, drop of control accuracy, even causes the resonance of train. In this paper, the thrust ripple produced by the cogging effect and flux linkage harmonics is analyzed. Then a method of harmonic current injection is proposed to compensate cogging force and reduce the thrust ripple, without influence the decoupling control of traction and suspension system. The injected current harmonics are controlled under multiple rotating reference frames independently. Finally, based on voltage equations of harmonics, the decoupled harmonic current controllers with harmonic voltage feedforward are designed, which improve the performance of current harmonics response and thrust ripple suppression. Simulation results on Simulink verify the effectiveness of proposed thrust ripple suppression method for LSLSM.