With the wide application of laser in the field of skin plastic surgery, micro laser galvanometer scanner has made great progress in this field with its portability. However, the measurement method used to measure the deflection angle of laser galvanometer in the narrow space of scanner with high precision remains to be studied. In this paper, an angle measurement method based on magnetic field is proposed, and the effect of the shapes of permanent magnets (PMs) on the measurement is studied by theoretical and experimental study under the condition that the maximum available space for the PMs is a 10 mm side cube. An angle measuring experimental device is set up, and the contrast experiment is carried out with different PMs which are the same as simulation. The experimental results show that cylindrical PM is more suitable than other PMs, which is consistent with the simulation results, and the maximum nonlinearity error is 0.562%. This method has the advantages of small volume, non-contact measurement, small moment of inertia, good dynamic response and no external excitation for the PMs, so it has a broad application prospect in micro laser galvanometer scanner.