Abstract: Bone infection is characterized by high incidence, complex pathogenic microorganisms, difficult treatment and poor prognosis. Rapid and accurate identification of pathogenic microorganisms and their targeted elimination are crucial for the complete treatment of bone infection. Metagenomic next-generation sequencing (mNGS), with its advantages of accuracy, high speed, efficiency and broader pathogen detection coverage compared to traditional bacterial culture, has been widely used in the clinical diagnosis of various infectious diseases. However, due to its unique detection mechanism, mNGS cannot provide antimicrobial susceptibility results, limiting its guidance for later targeted antimicrobial therapy. Phages, as viruses that specifically infect bacteria and other prokaryotes, can be analyzed and screened via mNGS. They exhibit high host specificity, typically infecting a single bacterial species, and do not require antimicrobial susceptibility data. Selecting one or more corresponding phages can effectively inhibit or eliminate the target pathogen. This paper reviews the advantages, limitations, future directions and guiding significance of mNGS and phage therapy in the diagnosis and treatment of bone infection.