The invention relates to a food-borne pathogenic microorganism detection method based on a microscopic multi-modal fusion spectrum technology. A set of new detection method of a microscopic multi-modal fusion spectrum is creatively provided, and a detection platform which is used for fast and high-throughput detection of food-borne pathogenic microorganisms is constructed. The food-borne pathogenic microorganism detection method comprises the following steps of firstly preparing base combination reinforcing labeled molecules and specific recognition molecules under an independent mode of a microscopic Raman spectrum, constructing a bio-labeled nanoprobe, specifically labeling microorganisms by utilizing the prepared bio-labeled nanoprobe, and collecting Raman spectra of different concentrations of food-borne pathogenic bacteria solutions; collecting near-infrared spectrum signals of different bacteria solutions under a microscopic near-infrared spectrum mode, mining characteristic variables which are closely related to the bacteria solutions by utilizing measures of intelligent search and data dimension reduction, fusing with a Raman labeled peak, establishing a standard curve of a relation of the fusion spectrum strength and the bacteria solution concentration, and realizing food-borne pathogenic microorganism specificity quantitative detection based on the fusion spectrum technology.