A re-sampling algorithm for smart substation protection data based on cubic spline interpolation value and time scale transformation is proposed in the paper.When the power system frequency shifts from nominal50Hz，the full-cycle sampled values in a data window of the Fourier algorithm are obtained by re-sampling so as to reduce the spectrum leakage error.The proposed algorithm also realizes sampling rate conversion from the fixed sampling rate of process level data to the sampling rate required by protection algorithms.The proposed re-sampling algorithm can efficiently reduce errors caused by lost or delayed sampled value on process bus in transmission.Simulation results based on MATLAB show that，the proposed re-sampling algorithm can realizeseamless connection”of sampled data with protection algorithms when merging units sampling data of transformers is mismatched to the protection algorithms.And simulation results of a power system fault model built by MATLAB/Simulink validate the effectiveness of the proposed algorithm applied to the protection of actual power systems.