The spin-exchange relaxation-free (SERF) magnetometer as an ultra-precision magnetometer has been researched during recent times. The sensitivity of the signal measurement limits the accuracy of the magnetometer. The optical modulation method is used to detect the tiny optical rotation angle of the linear polarized (LP) light, and the modulator is improving from Faraday magneto-optic modulator to photoelastic modulator (PEM). However, the current commercial PEMs have several defects in the adoption of the magnetometer. First, considerable heat will reduce the PEM’s modulation precision; In addition, the big appearance will hamper the assembly of the magnetometer; Moreover, the products are unreliable in the small amplitude modulation. In order to overcome these drawbacks, a sort of PEM is designed by theoretical calculation and finite element simulation in the paper. The target PEM with 50kHz intrinsic frequency and 795nm transmission is composed of one hexahedron piezoelectric transducer (PZT) glued with one optical glass each other. About the PZT, the alpha quartz is determined by considering the vibration and temperature properties of the material, then a proper cut angel and size is calculated to satisfy the design target. Subsequently, the fused silica is used for its well optical property. In the final, a simulation is conducted to verify the feasibility and validity of the design.