The invention proposes a method for compensating a residual magnetic field inside a magnetic shielding case of a laser atomic magnetometer so that the residual magnetic field inside the magnetic shielding case can be reduced or eliminated and thus the laser atomic magnetometer is able to measure the flux weakening with high sensitivity. The invention provides a method for compensating a residual magnetic field inside a magnetic shielding case of a laser atomic magnetometer, so that problems that the sensitivity of the laser atomic magnetometer is affected because the small-angle non-orthogonality of the three-axis coil exits and the laser propagation direction is not overlapped with the spindle of the magnetic field completely in the actual operation are solved. Internal currents in a three-axis coil are adjusted circularly by multiple times; observation and fitting of a laser atomic magnetometer signal are carried out; and the residual magnetic field strength at the alkali metal atomic vapor bubble inside the magnetic shielding case is reduced or eliminated finally.