This work proposes a novel method for in situ measurement of the non‐orthogonal angles of magnetic field coils based on single‐beam magnetic resonance. The orthogonality of magnetic field coils is crucial for ensuring the accuracy of atomic magnetometers. The theoretical principles are derived to establish a measurement method for the non‐orthogonal angles. The proposed method requires only one single beam of light to perform in situ measurements of non‐orthogonal angles in the YZ and XZ directions. The experimental results demonstrate that the angle between the Y and Z coils is 89.3001 ± 0.0045°, a value that remains stable despite variations in experimental parameters such as temperature and light power, thereby confirming the robustness of the method. Additionally, the measured gyromagnetic ratio is 6.9963 ± 0.0005 Hz nT−1, which closely matches the theoretical value of 6.9958 Hz nT−1, further validating the method's accuracy. The proposed method provides a more straightforward approach and has significant potential for widespread application across various atomic magnetometers, especially in miniaturized configurations. Furthermore, this method may be extended to the field of atomic gyroscopes.