The invention discloses a novel method for detecting pathogenic microorganisms. The method comprises: a collection step of samples such as 
cerebrospinal fluid and 
alveolar lavage fluid; a collection steps of 
peripheral blood samples; 
a DNA extraction step; a 
library construction step; a sequencing step; and an analysis step. The 
DNA extraction step comprises: taking 400 [mu]l sample for detection,adding reaction reagents of buffer GB, 
Lysis Enzyme K, 
RNA, Carrier to the sample, conducting reaction at 56 DEG C for 10 minutes to obtain a reaction solution, purifying the reaction solution by 
silica gel membrane adsorption column to remove salt ions and organic reagents, and obtaining 
DNA with total amount and purity meeting the requirements. The 
library construction step comprises: conducting terminal repair, 
linker connection, 
library amplification and enrichment, purification and 
quality control of the 
DNA to complete the library construction. The sequencing step comprises: denaturingthe library into a 
single strand by NaOH, then binding the library to a sequencing 
chip, enriching each 
single strand DNA into a cluster by bridge amplification, and obtaining 
sequencing data by usingIllumina SBS sequencing method to read the sequence. The analysis step comprises: filtering the 
sequencing data, removing the human source and the 
linker sequence, and comparing the remaining data with a microbial 
reference database.