The magnetic noise of a vehicle has a strong impact on the magnetic gradiometer, so a vehicle magnetic noise compensation method is proposed. Based on the production mechanism of the vehicle magnetic noise, a mathematic model for vehicle magnetic noise on the tetrahedron magnetic gradiometer is proposed, in which the difference algorithm of the magnetic gradiometer is used to fuse the magnetic noise of each vector magnetometer. In terms of this mathematic model, we propose the noise compensation algorithm and the compensation coefficients recognition method by using the mathematic relations of the 9 components of the magnetic gradient tensor. Simulation results show that the proposed method can efficiently compensate 95.9% vehicle magnetic noise on the magnetic gradiometer. This method can compensate vehicle magnetic noise on the magnetic gradiometer output directly by the compensation coefficients, and realize the holistic noise compensation of the magnetic gradiometer theoretically.