Abstract: OBJECTIVE To investigate the differential diagnosis of central nervous system infectious diseases with different pathogens by mNGS and traditional culture in cerebrospinal fluid. METHODS A total of 87 patients with central nervous system diseases admitted to the 928th Hospital of the Joint Logistics Support Force of the Chinese People's Liberation Army from Jun 2017 to Jun 2022 were recruited and divided into the viral encephalitis group (n=22), tuberculous meningitis group (n=29), suppurative meningitis group (n=23) and cryptococcal meningitis group (n=13) according to clinical diagnostic criteria. Cerebrospinal fluid of all patients were sent for mNGS and traditional bacterial culture. The sensitivity and specificity of the two methods for the diagnosis of neurological diseases with different pathogens were calculated and compared. RESULTS When the unique reads ≥2, mNGS of the viral encephalitis group had the sensitivity of 76.92%, specificity of 88.57%, and the sensitivity and specificity of the traditional culture were 32.69% and 74.29%, respectively. The sensitivity and specificity of mNGS for the detection of CSF unique reads >1 were 55.56% and 70.51%, respectively. When the sequence number of Mycobacterium tuberculosis was greater than 1, the sensitivity and specificity of traditional culture were 44.44% and 69.23% respectively. When the unique reads ≥5, the sensitivity of mNGS assay of the suppurative meningitis group was 71.43%,with the specificity of 90.91%; and the sensitivity and specificity of traditional culture were 47.62% and 65.15%, respectively. The sensitivity and specificity of Cryptococcal DNA detected by mNGS were 60.00% and 84.15%, respectively; and those by the traditional culture were 40.00% and 76.83%, respectively. CONCLUSION Compared with the traditional culture method, mNGS has significant advantages in the diagnosis of different pathogens in the identification of infection in central nervous system infectious diseases, providing a rapid, convenient and accurate method for the early diagnosis of central nervous system diseases.