With the widespread adoption of digital equipment in intelligent substations, testing digital signals in power systems has become an important role for relay protection test equipment. Testing and calibrating digital signals require high accuracy. However, existing methods have low precision, cannot be calibrated at full range for all indexes, and have complex configuration, making them unsuitable for routine calibration work. To solve the above problems, a novel calibration method is designed and implemented using field programmable gate array (FPGA) to achieve accurate input and output time control. Accurate calibration relies on multiple forms of traceability including theoretical value traceability based on waveform comparison, time scale value traceability based on accurate time stamps, and algorithm traceability based on typical algorithms. Compared with other existing methods, the proposed approach reduces the mean absolute error of action time and time measurement by 92.88%, effectively addressing a key industry challenge and offering a valuable reference for further research, application, and standardization.