The invention belongs to the technical field of bioinformatics and particularly discloses a method of screening multiple sclerosis biomarkers. The method includes: acquiring a data set GSE21942 from an GEO database, and subjecting a sample to MAS5 standardization by a GPL570 platform; removing x or y gene expressions invariable according to a formula: (|(x(i)+y(i))/(x(j)+y(j))-1|(delta(i, j=1, 2,..., N), and screening out mutually inhibiting gene pairs (x, y) to obtain a multiple sclerosis biomarker. Delta refers to degree of approximation between genes x and y, and is 0.08 in experiments; x(i) refers to gene expression quantity of the i-th sample of the gene x; y(i) refers to gene expression quantity of the i-th sample of the gene y. The mutually inhibiting gene pairs in mononuclear cells in peripheral blood of both normal people and MS patients to obtain the multiple sclerosis biomarker; by applying the screened multiple sclerosis biomarker in the study and analysis of biological significance, real conditions of the patients can be indicated.