〔Abstract〕 Objective To explore the application value of metagenomic second-generation sequencing(mNGS) in patients with suspected central nervous system(CNS) infection in the general intensive care unit(ICU), and to provide reference for rapid and accurate diagnosis of central nervous system infection patients in the general ICU. Methods The data of 82 patients who underwent cerebrospinal fluid mNGS examination in the general ICU of our hospital from 2018 to 2021 were collected. According to the inclusion criteria, 52 patients with suspected CNS infection, who had undergone routine biochemical and culture testing as well as mNGS on cerebrospinal fluid samples, were included in the final data analysis. The clinical diagnosis of CNS infection was taken as the "gold standard", and the application value of the two methods, traditional culture and mNGS, for clinical diagnosis were compared. Results Among the 52 patients, 32 were finally diagnosed with CNS infection, 24 of them were positive for mNGS in cerebrospinal fluid, and 5 were positive in culture of cerebrospinal fluid. The sensitivity and specificity of the two methods were 75.00% vs 15.63% and 55.00% vs 95.00%, The negative predictive values were 72.73% vs 83.33%, and 57.89% vs 41.00%, respectively; there was no significant difference in the detection rates between the two methods(P>0.05). Of the 32 patients with CNS infection, 14 had bacterial infection, 9 had viral infection, 2 had fungal infection and 7 had other pathogenic bacteria infection. The sensitivity of mNGS to detect pathogens of viral infection was 66.70%, the specificity was 95.30%, and the positive predictive value was 75.00%, and the negative predictive value was 93.20%, which was highly consistent with the gold standard of clinical final diagnosis(Kappa value=0.649, P<0.01). Conclusion Cerebrospinal fluid mNGS has a higher diagnostic accuracy for central viral infection compared to bacterial infection, and it is recommended to use mNGS for rapid screening of patients with suspected central virus infection.