The invention discloses a blood metagenome sequencing data analysis method and device and an application thereof. The blood metagenome sequencing data analysis method comprises a data quality controlstatistics and splitting step, a humanized sequence removal step, a plasmid sequence removal and internal reference comparison step, a pathogen genome sequence library comparison step and a pathogen parameter annotation step. The invention provides a blood flow infection detection device based on a blood metagenome sequencing data analysis method. According to the method and device provided by theinvention, the free nucleic acid sequences in blood are detected through a metagenome sequencing method, a bioinformatics analysis method is combined, more than 8,000 pathogenic microorganisms such as bacteria, viruses, fungi and parasites possibly existing in a blood flow infection patient body are detected at a time, and a detection result can be obtained within 24 hours at the soonest. The speed, the sensitivity, the accuracy and the efficiency of blood flow infection detection are greatly improved.