At present, the traceability of the analog-input merging unit calibrator still follows the method of tracing the traditional transformer calibrator, which has the problem of system error and unstable precision. Based on the working principle and characteristics of the merging unit calibrator, this paper the analyzes the error sources and proposes a traceability system for the analog-input merging unit calibrator based on digital differential method. The system constructs a 0.02 level standard merging unit with differential method, which provides traceability for the merging unit calibrator with accuracy of 0.05 level and below. The phase differential algorithm based on Hilbert transform in the system is superior to the precision of 〖10〗^(-10) minute, and does not affect the amplitude in the condition of frequency offset and harmonic. Compared with the existing traceability methods, the method has the advantages of simple structure, low cost and no environmental impact, and has good practical application value.