The adjustment of the natural frequency of a micro crystal resonator (MCR) is the key requirement in its manufacturing, which determines the actual performance of the product. Laser processing is a new method for MCR frequency modulation, and its process parameters directly affect the frequency modulation effect. Aiming at the laser processing equipment for MCR frequency modulation, the structure of the laser processing control system for MCR frequency modulation is designed by analyzing the requirements of a laser processing control system. The working flow of the laser processing control system for MCR frequency modulation is studied, the motion control method of the laser processing platform for MCR frequency modulation is proposed, and the laser processing control system for MCR frequency modulation is designed. By analyzing the laser characteristics for MCR frequency modulation, an orthogonal experiment is carried out to optimize the laser processing parameters for MCR frequency modulation.