Background Our understanding of sepsis-associated immune impairment is incomplete. The objective of this retrospective study was to investigate correlations of sepsis clinical manifestations with peripheral blood lymphocyte subpopulations in lymphocyte immunity. Methods Twenty individuals without sepsis and eighteen with sepsis were enrolled. Lymphocyte phenotypes (CD3+, CD4+, CD8+, CD3-CD16+CD56+, CD19+, CD4+CD25+CD127+, CD8+CD28-, and CD8+CD28+) were assessed by flow cytometry. Fresh fecal bacteria cue proportion was measured to determine intestinal dysbacteriosis. Results Compared with the non-sepsis group, the sepsis patients had clearly lower proportions of CD3+, CD4+ and CD8+CD28+ cells and substantially higher proportions of CD19+ cells (p<0.05). Among 38 patients with infection, CD4+ cells and CD8+CD28+ cells in a survivor group had significantly higher presence compared with patients who had died (p<0.05), The subgroup analysis results showed that CD4+ cells in the survivor subgroups were higher than those in the deceased subgroups (p<0.05). CD8+CD28+ cells in the non-sepsis survivor subgroup were higher than those in the deceased subgroups (p<0.05).. Bivariate correlation analysis showed that the intestinal dysbacteriosis was significantly correlated with the severity of sepsis and its prognosis (r2=0.2788, p=0.001, r2=0.1764, p=0.009, respectively). CD4+, CD19+, and CD8+CD28+ cells were significantly correlated with intestinal dysbacteriosis (r2=0.1024, p=0.049, r2=0.1063, p=0.046, r2=0.1909, p=0.006, respectively). Conclusions In conclusion, the lymphocyte populations of CD3+, CD4+, CD8+CD28+ and CD19+ cells were accessible for predicting the severity and mortality of sepsis patients. In addition, intestinal dysbacteriosis had a significant impact on the immune system of sepsis patients as revealed by peripheral blood lymphocyte population.