PIN is a common modulation structure in the electro-optic modulator, and the thermo-optic effect in work directly affects the performance of electro-optic modulator. In order to alleviate the thermo-optic effect, the principle of PIN modulation is firstly researched. A novel structure of waving PIN modulation based on silicon on insulator (SOI) material is invented, and the new structure is compared with ordinary PIN modulation structure. The influence of the waving PIN structure on temperature, refractive index, carrier concentration of modulation area are quantitatively analyzed. At 2 V voltage modulation through simulation, the temperature of waving PIN structure is reduced by 11.6%, the refractive index drift is reduced by 28% through restraining the thermo-optic effect, and injection carrier concentration of modulation area is increased by 26.7%. Finally, the waving PIN micro-ring electro-optic modulator and ordinary PIN micro-ring electro-optic modulator are respectively fabricated and tested. The test results show that the waving PIN structure has greater shift values of resonance peak and can effectively restrain the thermo-optic effect. The advancement of the novel structure and the correctness of theoretical analysis are verified.