The invention provides a method and a system for improving simulation accuracy of a controller HIL (hardware-in-the-loop) simulation system. A control algorithm in the controller HIL simulation system is compiled and responded, an electrical and electronic simulation module is controlled, a PWM (pulse-width modulation) digital pulse signal output by a master control device is subjected to high-frequency filtering, a modulated wave is generated and compared with a carrier signal generated by an RTDS (Real Time Digital Simulator) in a small-step simulation mode, a control signal of the electrical and electronic simulation module is obtained, electrical parameters and control parameters of the controller HIL simulation system are set, and the controller HIL simulation system is operated. In the whole process, the PWM digital pulse signal output by the master control device is subjected to high-frequency filtering, the modulated wave is generated and compared with the carrier signal generated in the small-step simulation mode, the controller HIL simulation system is controlled through the modulated wave, sampling errors are reduced, and accuracy and reliability of the controller HIL simulation system are improved.