Objective:To investigate the effects of Yishen Decoction via colonic dialysis on intestinal flora and microinflammation in patients with chronic kidney disease (CKD) stages 3-5. Methods:A total of 156 patients with stage 3-5 CKD from the Second Affiliated Hospital of Guizhou University of Chinese medicine from October 2019 to October 2020 who met the inclusion criteria were divided into 2 groups of 78 patients according to the random number table method. The control group was given colonic dialysis treatment, the treatment group was given Yishen Decoction transcolonic dialysis treatment on the basis of the control group, and both groups were treated for 8 weeks. TCM syndrome scores were performed before and after treatment, serum levels of CRP, IL-6, and TNF-α were measured by ELISA, and SCR, BUN, and uric acid (UA) levels were detected by a fully automated biochemical analyzer. Fresh feces were collected from the patients, anaerobic culture and aerobic culture were performed, and the numbers of Bifidobacterium, Lactobacillus acidophilus, and Escherichia coli were counted to evaluate the clinical efficacy. Results:The total effective rate was 97.4% (76/78) in the treatment group and 84.6% (66/78) in the control group, and the difference was statistically significant ( χ2=7.847, P=0.005). At 4 and 8 weeks after treatment, the scores of lumbar and knee tenderness( t=6.596, 8.792), eating less and being dull ( t=12.060, 24.140) and pale complexion ( t=7.983, 12.300) in the treatment group were significantly lower than those in the control group ( P<0.01); the levels of bifidobacterium ( t=4.037, 2.358) and Lactobacillus acidophilus ( t=7.352, 2.092) were significantly higher than those in the control group, while the levels of Escherichia coli ( t=3.822, 6.084) were significantly lower than those in the control group ( P<0.01 or P<0.05). The serum CRP ( t=9.326, 12.300), IL-6 ( t=4.591, 4.716), TNF-α ( t=9.304, 9.775), SCr ( t=17.630, 11.530), BUN ( t=2.674, 2.248), UA ( t=10.860, 13.160) were significantly lower than those in the control group ( P<0.01 or P<0.05). Conclusion:Yishen Decoction can improve intestinal microecological status, inhibit microinflammatory response and relieve clinical symptoms for the patients with stage 3-5 CKD.