Objective By using metagenomic next-generation sequencing (mNGS), we aimed to analyze the microbes characteristics of lower respiratory tract of patients with pulmonary infection, so as to improve the further understanding of clinical etiological characteristics of patients with pulmonary infection. Methods A total of 840 patients with suspected pulmonary infection were enrolled from August 2020 to October 2021 in West China Hospital of Sichuan University. mNGS was used to detect the microbiome of bronchoalveolar lavage fluid of all patients, and the microbial characteristics of lower respiratory tract of all patients were retrospectively analyzed. Results A total of 840 patients were enrolled, of which 743 were positive for microbiome, with bacterial infection accounting for 35.13% (261/743). Acinetobacter baumannii accounted for 18.98% (141/743), followed by Streptococcus pneumoniae (14.13%, 105/743), Klebsiella pneumoniae (13.46%, 100/743), Enterococcus faecium (12.11%, 90/743) and Mycobacterium tuberculosis complex (11.98%, 89/743). Acinetobacter baumannii had the highest average reads (2607.48). In addition, some specific pathogens were detected, such as 9 cases of Chlamydia psittaci. The main fungal infections were Candida albicans (12.38%, 92/743), Pneumocystis jirovecii (9.02%, 67/743) and Aspergillus fumigatus (7.40%, 55/743), among which the average reads of Pneumocystis jirovecii was higher (141.86) than Candida albicans and Aspergillus fumigatus. In addition, some special pathogens were also detected, such as a case of Talaromyces marneffei. The main viral infections included human β herpevirus 5 (17.90%, 133/743), human γ herpevirus 4 (17.36%, 129/743), human β herpevirus 7 (16.15%, 120/743) and human α herpevirus 1 (13.59%, 101/743), among which the average reads of human herpesvirus type 1 (367.27) was the highest. Parasitic infection was least, with only 2 cases of Echinococcus multilocularis, 2 cases of Angiostrongylus cantonensis, 2 cases of Dermatophagoides pteronyssinus and 1 case of Dermatophagoides farinae, which were mainly infected with bacteria and viruses. In addition, a total of 407 patients were diagnosed with mixed infection, of which virus and bacteria mixed infection was the most (22.61%, 168/743). The distribution of microorganisms in different seasons also has certain characteristics. For example, bacteria (Acinetobacter baumannii) were most frequently detected in autumn and winter, while viruses (human gamma-herpesvirus type 4) were most frequently detected in spring and summer. Conclusions In the lower respiratory tract of patients with pulmonary infection, the main gram-negative bacteria are Acinetobacter baumannii and Klebsiella pneumoniae, while the main gram-positive bacteria are Streptococcus pneumoniae, Enterococcus faecium and Mycobacterium tuberculosis complex; the main fungi are Candida albicans, Pneumocystis jirovecii and Aspergillus fumigatus; the main viruses are human β herpevirus 5, human γ herpevirus 4 and human β herpevirus 7. However, parasites are rarely detected and have no obvious characteristics. Bacterial infection and bacterial virus mixed infection are the main co-infections; the microbial characteristics of autumn and winter are different from those of spring and summer. In addition, attention should be paid to special pathogenic microorganisms, such as Chlamydia psittaci and Talaromyces marneffei. These characteristics could be used as reference and basis for the pathogenic diagnosis of pulmonary infection.