Objective To explore the effects of Gancao Xiexin decoction(GXD)on aquaporin(AQP)3 and AQP4 in rats with ulcerative colitis(UC). Methods Thirty-two clean SD rats, eight SD rats were used as the blank group, the remaining 24 rats were used to replicate the UC model with 4% dextran sulfate sodium. After the model was successful, the rats were divided into model, Western medicine(slow-release mesalazine granules), and Chinese medicine(Gancao Xiexin decoction)groups, eight rats in each group and then gavaged continuously for 2 weeks once a day. Body mass, disease +activity index, colon length, colonic mucosa damage index, histopathological changes, histological damage index, serum tumor necrosis factor-α (TNF-α), interleukin-(IL)-1β, IL-6 and colonic AQP3 and AQP4 were assessed. Results Compared with the blank group, serum levels of TNF-α, IL-1β, and IL-6 in model and administration groups were increased(P<0. 05), colonic AQP3 and AQP4 levels in model and administration groups were decreased(P<0. 05), and colonic AQP3 mRNA levels in model and administration groups, and AQP4 mRNA levels in model and Western medicine groups were declined(P< 0. 05). There was no remarkable difference in mRNA expression of colonic AQP4 between Chinese medicine and blank groups(P>0. 05). Compared with the model group, serum levels of TNF-α, IL-1β, and IL-6 in Western and Chinese medicine groups were decreased(P<0. 05), serum levels of TNF-α, IL-1β and IL-6 in the Chinese medicine group were lower than those in the Western medicine group(P<0. 05), colonic AQP3 and AQP4 protein and mRNA levels in administration groups were increased(P<0. 05), the colonic AQP4 protein level in the Chinese medicine group was higher than that in the Western medicine group(P<0. 05), and colonic AQP3 and AQP4 mRNA levels in the Chinese medicine group were higher than those in the Western medicine group(P<0. 05). Conclusions GXD effectively improves the body weight, disease activity index, colonic mucosa damage index, and histological damage index of UC rats, which may regulate serum TNF-α, IL-1β, and IL-6 levels by improving AQP3 and AQP4 protein and mRNA levels in the colon, which may be the mechanism of GXD in for UC treatment.