During the active phase of ulcerative colitis (UC), mitochondrial autophagy is an important antagonistic mechanism. Our investigation examines the regulatory effect of Dima decoction on UC inflammation via the autophagy pathway. SD rats were divided into 5 groups (n = 10): normal control (NC) model, mesalazine, Dima decoction treatment and Dima decoction combined with YC-1 (inhibitor) group. Results showed that treatment of Dima decoction effectively ameliorated the symptoms of UC. Drug-containing serum from Dima decoction treated rats leads to an significantly increase in IL-4 and IL-10 content in HT-29 cells, while also causing a decrease in IL-1β and IL-6 content. Moreover, protein level and mRNA level of HIF-1α, BNIP3, Beclin-1 were obviously up-regulated. In addition, protein level of LC3B II and the ratio of LC3B II/I were dramatically promoted after Dima decoction serum administration. The protein level of Bax was notably decreased in TH-29 cells after Dima decoction serum supplement, while that of Bcl-xl was remarkably up-regulated. In conclusion, Dima decoction significantly alleviated the symptoms of UC. The regulation could involve modulation of the hypoxia-inducible HIF-1 α/BNIP3/Buclin-1 pathways, leading to effects on mitochondrial autophagy and inflammation. These findings offer new insights into the mechanism of Dima decoction for treating UC.