The invention relates to a metagenomics-based pathogen analysis method and device, equipment and a storage medium. According to the metagenomics-based automatic pathogen analysis method provided by the invention, on one hand, the flow and tools of a data analysis method are integrated and optimized, and the pathogen identification process is standardized, so that the data analysis time can be greatly shortened, the clinical detection period can be shortened, and rapid detection can be realized; and on the other hand, a platform effectively distinguishes pathogenic bacteria from background bacteria by establishing a microorganism reference sequence database and a pathogen information base and comprehensively evaluating parameters and evidence grades, so that missing detection caused by non-coverage can be effectively prevented, and the reference significance and interpretability of clinical detection results are further improved.