By the analysis of the mathematical principle and frequency spectrum characteristics of the full wave Fourier algorithm, and the simulation of MATLAB mathematical model, the feasibility of the algorithm was demonstrated in the microcomputer based relay protection unit. Secondly, by the microcomputer relay protection unit and vehicle test, the full wave Fourier algorithm was verified with strong filtering performance, which could avoid the influence of other integer harmonic components while calculating the integer harmonics, meeting the application requirements of railway passenger vehicle microcomputer relay protection unit.