In intelligent substation, the introduction of digital protection devices such as merging unit, intelligent terminal, etc. prolongs the operation time of protection, which brings the safe threat to the cutoff of power system fault. Therefore, it is necessary to analyze the time delay link of protection operating time in intelligent substation. In this paper, the composition of time delay in intelligent substation is given, and the difference of each part between intelligent and traditional substation is analyzed. Further, the two major compositions of time delay in sampling and intelligent terminal link are analyzed in detail, the deep mechanism of time delay phenomenon is given and the effective measures to reduce the time delay in each link are discussed. Finally, the differences of operation time delay between traditional and intelligent substation are compared by experiment, and the results testify the validity of theoretical analysis.