The present study aimed to evaluate the impact of hydroxychloroquine (HCQ) on the mucosal barrier and gut microbiota during the healing of mice colitis. The body weight, colon length, colon Hematoxylin-Eosin (H&E) staining, occult blood in feces and serum inflammatory factor levels were measured to evaluate the function of HCQ on inflammatory process in colitis mice. The Alcian blue staining, immunohistochemistry, immunofluorescence and serum FITC-Dextran assay were performed to assess the intestinal mucosal permeability. And the composition and expression differences of intestinal microorganisms in feces were analyzed with 16S rDNA sequencing for exploration of HCQ impact on gut microbiota in colitis. The results showed that the administration of HCQ did not significantly alter the body weight, colon length, or fecal occult blood of the mice. However, HCQ treatment did lead to recovery of the structure and morphology of the intestinal mucosa, increased expression of tight junction proteins (E-cadherin and Occludin), decreased permeability of the intestinal mucosal barrier, increased serum IL-10, and decreased level of tumor necrosis factor-alpha (TNF-α). Additionally, HCQ was found to increase the abundance of Euryarchaeota, Lactobacillus_murinus and Clostridium_fusiformis, while decreasing the abundance of Oscillibacter, uncultured_Odoribacter, Bacterioidetes and Muribaculum. These findings support that HCQ plays a role in the treatment of mice colitis possibly by altering the gut microbiota.