Objective: To investigate the clinical value of metagenomic next-generation sequencing (mNGS) in the diagnosis of intracranial infection after neurosurgery. Methods: Fifteen patients suspected of intracranial infection after neurosurgery were prospectively enrolled in Department of Neurosurgery of Xuanwu Hospital of Capital Medical University from January to October, 2019. Two weeks later, three neurosurgeons analyzed and judged whether it was clinical intracranial infection. The cerebrospinal fluild (CSF) routine, biochemical, bacterial smear and culture were recorded. The same CSF sample was sent for mNGS. All cases were followed up for 3 months, and the final diagnosis and treatment outcome were recorded. Results: Eight cases were clinically diagnosed as intracranial infection. Among them positive for bacterial culture and mNGS, 3 cases were negative for both, one case was positive for bacterial smear in CSF at the early stage, but negative for culture and mNGS. Diagnosis of intracranial infection were excluded in 7 cases clinically. All the 7 cases were negative for bacterial culture and mNGS, one case was positive for bacterial culture of Staphylococcus epidermidis with head of ventricular drainage tube, and negative for bacterial culture and mNGS in CSF. The bed was judged to be contaminated by the tube head specimen. The number of detection sequence of pathogenic bacteria genes in the 4 cases with positive mNGS was 212, 329, 1601 and 5371, which was accompanied by the decrease of glucose and the increase of leukocyte in CSF. The number of gene sequences of non-infectious background bacteria was less than 100. The sensitivity and specificity of mNGS sequencing in the diagnosis of postoperative intracranial infection were 4/8 and 7/7, and the accuracy was 11/15. Conclusions: The clinical value of mNGS in the diagnosis and treatment of intracranial infection after neurosurgery is preliminarily verified. Based on the traditional detection method, mNGS in CSF can be used as a supplement, but the detection of mNGS must be interpreted reasonably according to the clinical situation. Copyright © 2020 by the Editorial Board of Chinese Journal of Contemporary Neurology and Neurosurgery.