Central nervous system (CNS) infection is a common nervous system acute and severe disease, mainly manifested as encephalitis, meningitis and meningoencephalitis, but also manifested as brain abscess and brain granuloma et al. The basis for the diagnosis of CNS infection lies in the detection of pathogens from brain parenchyma or cerebellar spinal fluid (CSF). However, CSF is relatively difficult to obtain and the sample size is small, which limits the rapid and definite diagnosis of CNS infection pathogens. In addition, CNS infection usually has non-specific clinical manifestations, so it is difficult to identify the pathogen for about half of CNS infection. Metagenomic next generation sequencing (mNGS) and biochip technology provide new means to identify the pathogens of CNS infection. This study analyzes the incidence and epidemic characteristics of CNS infection in China, to standardize the CSF sample processing process, shorten the detection time, increase the sensitivity and specificity of pathogen detection, reduce the detection cost, identify the common pathogens of CNS infection, and establish a standardized rapid diagnosis system, effective prevention and control system.