The purpose of the present study is to explore the correlation between serum soluble myeloid cell trigger receptor 1 (sTREM1), procalcitonin (PCT), nuclear factor­κB (NF­κB) levels and intestinal microflora disorders in the patients with sepsis. A total of 86 patients with sepsis from Department of Digestive Medicine, Chongqing Qijiang District People’s Hospital were enrolled in the sepsis group. Fifty patients without sepsis admitted to the hospital during the same period were enrolled in the non­sepsis group, and 50 healthy people who underwent medical examinations in the hospital during the same period were enrolled in the control group. The alpha diversity and composition of intestinal flora, levels of serum sTREM1, PCT, NF­κB were analyzed. Spearman correlation analysis was performed. The results showed that Ace index, Chao index and Shannon index in the sepsis group were significantly lower, and Simpson index was significantly higher than those in the non­sepsis group and control group (P<0.05). The contents of Bacteroides and Bifidobacterium in the sepsis group were significantly lower, and the contents of Enterococcus, Escherichia coli, Staphylococcus were significantly higher than those in the non­sepsis group and control group (P<0.05). Serum sTREM1, PCT and NF­κB levels in the sepsis group were significantly higher than those in the non­sepsis group and control group (P<0.05). Spearman correlation analysis showed that serum sTREM1, PCT, NF­κB levels were negatively correlated with Ace index, Chao index, Shannon index (P<0.05), and positively correlated with Simpson index (P<0.05). It is suggested that serum sTREM1, PCT and NF­κB levels are associated with intestinal dysbacteriosis in the patients with sepsis.