The invention provides an early-stage pathogenic factor detection method based on gene co-expression network spreading analysis. The method comprises the following steps that: 1) obtaining data from the true gene expression of the case group and the control group of a certain disease, and preprocessing the gene expression data of a certain disease; 2) through correlation analysis, determining whether two genes have a coexpression relationship or not so as to establish a gene coexpression network; 3) finding a fault node set from the differential expression soring of the gene; and 4) calculating an average distance of the nodes of a fault node subset and a prepared fault spreading center, finding an incremental average distance sequence, and determining a dynamic network biomarker. The method aims at the detection problem of the early-stage pathogenic factor of a complex disease to put forward the early-stage pathogenic factor detection method based on gene co-expression network spreading analysis from the perspective of a system in order to make up the deficiencies of a traditional molecular biomarker and a statistic network biomarker, the early-stage pathogenic factor of a disease can be effectively found, and a contribution is made for accurate medical treatment.