In this paper, 16S rDNA sequencing technology was used to analyze the bacterial population composition in the sputum of patients with severe pneumonia. 16S rDNA sequencing technology is a bright spot in the development of modern molecular biology technology. 16S rDNA sequencing analysis is characterized by high sequencing flux, large amount of data obtained, short cycle, and more comprehensive reflection of microbial community species composition, real species distribution and abundance information. The length of 16S rRNA is about 1500 bp, and it is often used as the basis for bacterial taxonomy studies. 16S rDNA is the gene encoding the small subunit rRNA (16S rRNA) of the prokaryotic ribosome. Therefore, there is an urgent need for new clinical detection techniques in early diagnosis of pneumonia to change the status quo. Its outcome is closely related to bacterial pathogenicity and the timeliness and pertinence of antibiotic treatment, so early diagnosis is of great significance to the prognosis of patients. The diagnosis of pathogenic bacteria in severe pneumonia is difficult and the prognosis is poor. Pneumonia is one of the clinical very common respiratory infectious diseases, due to the lack of typical symptoms and signs in the early diagnosis of experience after antibiotic treatment inappropriate often makes pneumonia in delay no more waiting for a reason, and gradually develops severe pneumonia (severe root, SP), also called toxic pneumonia or explosive pneumonia, which is the highest rates of pneumonia types. In this paper, 16S rDNA sequencing technology was used to analyze the bacterial population composition in the sputum of severe pneumonia, and to explore a new method of etiological diagnosis. Sequencing analysis with 16S rDNA sequencing technology has the characteristics of high sequencing flux, large amount of data obtained, short cycle, and can more comprehensively reflect the species composition of microbial community, real species distribution and abundance information. With the continuous application of new molecular biology techniques in clinical detection, the classification of bacteria and microorganisms has deepened from the identification of phenotypic characteristics to the classification of gene characteristics. However, due to the long time of bacterial culture, the early use of antibiotics, the change of bacteria species, mixed infection and other problems, the results of bacterial culture in sputum are often false negative. Sputum examination and culture is the gold standard for the diagnosis of pathogens of severe pneumonia. Therefore, early diagnosis is of great significance to the prognosis of patients. Its outcome is closely related to bacterial pathogenicity and the timeliness and pertinence of antibiotic treatment.