Due to various nonlinear factors in an ordinary electromagnetic vibrator, the distortion of its output vibration waveform will always happen, especially at low frequencies (≤20 Hz), which blocks its application in a lot of area. To improve the acceleration waveform precision and reduce distortions at low frequencies, a waveform harmonic suppression method for low-frequency electromagnetic vibrators is proposed. After extracting the harmonic components in the output acceleration waveforms, a digital composite signal with harmonic compensation components is prospected according to the frequency response characteristic of the vibrator, and then sent back to drive the vibrator, which results in that the harmonic components in the formal waveform is suppressed. The proposed method was verified by simulations and experiments, and results show that the total harmonic distortions (THDs) of accelerations are reduced effectively at low frequencies, typically from 23% to less than 2% at the frequency as low as 0.1 Hz. The method is stable and robust because there is no real-time feedback loop in the system.