•For measuring the magnetic field strength of the micro-coil in the WP-μMS (structure: transmitting coil-micro-coil).•The calculation of the magnetic field strength is obtained through the mutual inductance coefficient.•Increase the mutual inductance measurement to nH-scale by using magnetically coupled resonance.•The magnetic field of the micro-coil is measured by eliminating magnetic field interference from the transmitting coil. In recent years, the wireless passive micro-magnetic stimulator (WP-μMS) has emerged as a focal for implantable neuromagnetism modulation research. However, accurately measuring the magnetic field strength of the micro-coil presents a significant challenge due to its small size and low mutual inductance (M). Firstly, this paper establishes a theoretical model of magnetic coupling with a three-stage structure of transmitting coil-micro-coil-detecting coil. The calculation method of detecting the coil to measure the magnetic field is determined by calculating the M between each pair of coils. Secondly, the magnetic coupling resonance method enhances the measured value M to the nH-scale. This approach also eliminates the influence of the M between the transmitting coil-detecting coil on the measurement of the transmitting coil-micro-coil M, thereby achieving accurate measurement of the mT-scale magnetic field strength of the WP-μMS micro-coil. Finally, the effectiveness of the measured mT-scale magnitude magnetic stimulation is validated biologically.