To investigate the diversity and composition of gut microbiota in patients with lung adenocarcinoma and lung squamous cell carcinoma. A single-center and case-control study was conducted to consecutively enroll a total of 27 lung cancer patients, including 15 males and 12 females, who were seen at the Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine between September 2018 to October 2020. A total of 20 cases of healthy healthy physical examiners, including 9 males and 11 females were recruited as healthy control group (HC) during the same period. Clinical data and stool samples were collected from each participants, and lung cancer patients were divided into lung adenocarcinoma group (AC, 19 patients, 8 males and 11 females) and lung squamous cell carcinoma group (SCC, 8 patients, 7 males and 1 females) according to the pathology type. Genomic DNA were extracted to amplify 16S rDNA V3-V4 region, then the Illumina MiSeq high-throughput sequencing platform and QIIME software were used for sequencing and analyzing the structure of the gut microbiota, respectively. Analysis of variance, χ test, K-W test were used to analyze the differences in age, gender,α diversity, and relative abundance of microbiota among the three groups. AC, SCC, and HC were aged (58.74±9.27), (63.38±6.12), and (55.65±7.79) years old, respectively. There were no difference in gender and age among the three groups (gender and age are respectively:χ=5.155, =0.076;=2.598,=0.086). And no significant difference in alpha diversity were found among the three groups (Chao and Shannon index were respectively: =0.616, =0.545; =2.484, =0.095), while β-diversity analysis indicated significant differences in the structure of intestinal flora among AC, SCC and HC (=0.001). LEfSe analysis showed that AC and SCC both have dominant bacterials. (=7.855,=0.020) and (=7.426,=0.024) were enriched in patients with AC, while (=8.400, =0.015), (=9.957,=0.007), and (=10.514,=0.005) were enriched in patients with SCC. Lung cancer patients have gut microbiota imbalance, while lung adenocarcinoma and lung squamous cell carcinoma patients have no significant difference in gut microbiota diversity, but lung adenocarcinoma and lung squamous cell carcinoma have their own unique microbiota. This imbalance of the intestinal microenvironment is of great significance for studying the occurrence and development of different pathological types of lung cancer.