Magnetoencephalography (MEG) system based on optically pumped magnetometers (OPMs) requires a magnetically shielded room (MSR) to establish a stable near-zero field environment. Affected by external environmental electromagnetic interference, the magnetic noise in the MSR will become very severe. In order to overcome this problem, this paper proposes a method for dynamic stabilisation of magnetic fields measured inside a MSR using an external coil system. Firstly, the field form of the external compensation coil was analysed by taking the AC characteristics of the material into consideration. Then, the linear characteristic of the control system is studied and a high performance magnetic noise suppression controller is designed based on the environment noise characteristics. Finally, simulation and experimental are carried out through a self-developed 1250 mm × 1250 mm × 2100 mm MSR, which indicates that the proposed method can effectively suppress dynamic magnetic fluctuation and noise.