The invention discloses a constructing method of a central system infection pathogen detection library based on high-throughput sequencing, a detection method and a kit. The library construction method comprises the following steps: extracting deoxyribonucleic acid (DNA) from a sample, and fragmenting the DNA to obtain a segmented DNA sequence; adding the segmented DNA sequence into a tail end repairing system to carry out a tail end repairing reaction, directly adding a linker sequence, a connecting enzyme, adenosine triphosphate (ATP) and polyethylene glycol into the reaction system after the tail end repairing reaction is completed, taking the ATP as an auxiliary enzyme under the action of the connecting enzyme to catalyze the linker sequence to be connected to two ends of the product of the tail end repairing reaction, so that a linker connecting product is obtained; and purifying the linker connecting product, and adding a nucleic acid single chain which is complementary to two ends of the linker sequence and used as a primer for polymerase chain reaction (PCR) amplification. The method can be used to realize rapid and broad-spectrum central system infection pathogen microorganism detection, too much pre-known clinical information of detection samples is not needed, detection can be carried out quickly and efficiently, the detection result is free of deviation, and a problem that the library construction failure rate of low-concentration cerebrospinal fluid samples is high can be solved.