Micro-magnetic stimulation is a research hotspot in the field of neuromodulation. However, it is difficult to measure the weak magnetic field produced by a millimeter-sized inductor. In this study, a mutual inductance model considering different positions and sizes was established for a common planar square spiral coil micro-magnetic stimulator. A physical model was simulated using the Comsol finite element method to verify the accuracy of the mutual inductance model. A weak magnetic field detection system was constructed using the TI AD8130 and NE5532 chips, and the magnetic field strengths of excitation micro-coils sized 3.612 × 3.612 and 5.55 × 5.55 mm 2 were measured. The results show that when the size ratio of the detection coil (DC) to the excitation coil (EC) is under a specific ratio (DC:EC = 1:1, 2:1, 1.53:1,2.36:1), the measurement range of the magnetic field strength is in the range 0-3.06 mT with an error of 0.05 mT, and the frequency is in the range 1-120 kHz. The measurement accuracy rate reaches 97.62%. The results of this study have potential application in the measurement of the weak magnetic field.