Abstract: Near-field effects are liable to rise in magnetotelluric signals due to noise, which seriously affects the quality of the collected signals. The widely used remote reference method-Robust-still has some shortcomings in suppressing near-field interference. In this paper, after being verified using numerical simulation in terms of denoising effects, the Hilbert-Huang transform (HHT) was applied to a magnetotelluric signal with serious near-field interference, achieving remarkable effects. Meanwhile, the polarization distribution of the electric and magnetic fields was calculated using the distribution function of polarization directions. It was found that the distribution function was closer to a Gaussian distribution function, also verifying the effectiveness of the HHT in suppressing near-field interference.