The invention provides a full-tensor space gradient compensation method and system used for biomagnetic detection. The method includes the steps of determining 9 full-tensor first-order gradient components of an environment magnetic field to be the first-order gradient components, in the x direction, the y direction and the z direction respectively, of the x-direction magnetic field, the first-order gradient components, in the x direction, the y direction and the z direction respectively, of the y-direction magnetic field and the first-order gradient components, in the x direction, the y direction and the z direction respectively, of the z-direction magnetic field according to a three-dimensional rectangular coordinate system xyz, determining 5 independent first-order gradient components in the full-tensor first-order gradient components, establishing the 5 independent first-order gradient components through a magnetometer, conducting compensation on a signal channel of the environment magnetic field, obtaining a compensation coefficient through the minimum mean square error, and achieving the compensation for the full-tensor first-order gradient components of the signal channel of the environment magnetic field. By means of the method and the system, the space full-tensor first-order gradient compensation is achieved, the environment noise can be more effectively restrained, and the noise restraining performance of a gradiometer is improved.