In the smart substation, data collected from any place is available for the entire substation' is required by data acquisition of merging unit. Therefore, the digital interface of merging units should possess the sampling rate conversion function and meet the demand of differential protection. This paper studies the mechanism of sampling rate conversion with cascade connection of decimation and interpolation. Also, the impacts of sampling rate conversion on differential current of differential protection is analyzed. To reduce group delay of high order Finite Impulse Response (FIR) in sampling rate conversion, a zero phase filtering algorithm is designed. Combining this algorithm with decimation and interpolation algorithm, the data from ECTs with different sampling rates can be converted to the same one. This achieves a unified sampling rate and improves the action speed of differential protection.