ObjectiveTo Explore the clinical value of metagenomic second-generation sequencing technology （mNGS） in the diagnosis and treatment of pulmonary infections after kidney transplantation， and to provide reference for precise diagnosis and treatment of diseases. MethodsThe clinical data of 124 kidneytransplant recipients with pulmonary infections were completed from the Department of Transplantation of the People's Hospital of Guangxi Zhuang Autonomous Region from January 1，2020 to December 15，2023. According to the pathogen detection method of mNGS， the patients were divided into sequencing group （60 cases） and traditional group （64 cases）. The pathogen detection rate， antibiotic use intensity， hospitalization time， hospitalization cost， non-invasive respiratory support rate， disease grade， severe illness rate， mortality rate， and other indicators were retrospectively analyzed between traditional group and sequencing group. ResultsThere was no statistically significant difference in gender， age，postoperative onset time， underlying disease， admission status of pulmonary infection （SMART-COP score）， pre-treatment creatinine， tacrolimus concentration， and methylprednisolone regimen between the two groups of patients （P＞0.05）. The detection of pathogens and mixed pulmonary infections in the sequencing group was significantly higher than that in the traditional group （P ＜ 0.05）. However， there was no statistically significant difference in the results of traditional detection methods between the two groups （P＞0.05）. There was statistically significant difference in the bronchoalveolar lavage fluid pathogens， mixed lung infections， pneumocystis jejun between the mNGS and culture + smear methods （P＜0.05）. One adverse reaction occurred in the sequencing group， with no complications related to bronchoscopy， and two adverse reactions occurred in the traditional group. In the sequencing group， the intensity of antibiotic use， mortality，peak pulmonary infection progression， discharge creatinine， length of hospital stay， and hospitalization costs were significantly lower than those of the traditional group （P ＜ 0.05）， and the non-invasive respiratory support for patients and critically ill patients were similar to the traditional group （P＞0.05）. ConclusionmNGS can provide precise directions for the diagnosis and treatment of kidney transplant recipients with pulmonary infections， it improves patient clinical prognosis， and is worthy of clinical promotion.