The invention discloses a pyrophosphate detection kit for common pathogens and drug-resistant genomes and its detection method and application, wherein the kit is used to detect 12 drug-resistant bacterial strains and drug-resistant genes in samples to be tested, Including Pseudomonas aeruginosa, Acinetobacter baumannii, Staphylococcus aureus, Klebsiella pneumoniae, Stenotrophomonas maltophilia, Escherichia coli, Enterococcus faecalis, Enterococcus faecium, KPC gene, The genotypes of OXA-23 gene, SHV gene and MecA gene, the kit includes amplification primer set, sequencing primer set, amplification solution, amplification enzyme and sequencing substrate. The present invention uses the pyrosequencing method to detect 12 highly pathogenic and high-detection rate pathogenic bacteria and drug-resistant genes at the same time. Detection, the detection process is flexible and simple, and the pyrosequencing results are fast and readable.