In smart substation, there is rated delay time in data sampling and outputting process of merging unit (MU), which directly relates with the time of relay protection. Currently, there is shortage in rated delay time measuring and threatens the normal system operation. In this paper, the group and transfer delay time are analyzed in the sampling, processing link of MU starting from sampling link. The research results show that the group delay time in time domain corresponds to linear phase characteristics in frequency domain. On that basis, the rated delay time measuring method based on frequency domain identification is proposed by inputting different frequency signals and obtaining phase frequency characteristics of MU. Meanwhile, the influences of MU phase error on the measuring of rated delay time are analyzed. Finally, the feasibility and validity of rated delay time method is verified by theoretical simulation and experiment measuring. The method in this paper provides a feasible way to measure delay time in digital sampling engineering application, and ensures the validity and reliability of relay protection.