In this study, we demonstrate a three-axis synchronous sweeping field (TSSF) method for in situ magnetic field compensation under three-axis nonorthogonal conditions for optically pumped magnetometers (OPMs). The OPM operated in the spin-exchange relaxation-free (SERF) regime is gaining popularity as a promising substitute for the superconducting quantum interference device (SQUID) in biomagnetism measurements. Nevertheless, the three-axis nonorthogonality inherent in the OPM will give rise to residual magnetic field inaccuracies along the pumping axis while conducting the in situ magnetic field compensation procedure, consequently introducing supplementary OPM errors. The TSSF method can more proficiently rectify the residual magnetic field along the pumping axis and suppress the corresponding errors. In contrast to traditional methods, the TSSF method diminishes both the rotation angles of the sensitive axis and dual-axis coupling coefficients, which are introduced through compensation errors along the pumping axis, by more than 80%, and improves the measurement sensitivities by more than 30%. This effective magnetic field compensation method of the OPM holds promise for further improving the performance of OPM. It is expected to enhance the localization and calibration accuracy of multiple-channel OPM-based magnetoencephalography (OPM-MEG) systems.