Sepsis is an important clinical problem in intensive care units, and lead to significant high morbidity and mortality. Early detection of pathogen is crucial for the implementation of targeted treatment and improvement of prognosis. However, the current pathogenic detection techniques are still lack of timeliness and accuracy. High-throughput sequencing technique may overcome these shortcomings, and is gradually being applied in the hospitals. However, it also has a series of disadvantages. This article will review the value of this technique in the detection of sepsis pathogen and the related advantages and disadvantages.