Objective To investigate the protective effect of emodin combined with cytokines on intestinal stress injury induced by hypoxia through autophagy. Methods Rat intestinal epithelial cells (IEC-6) were divided into five groups: BC group (IEC-6 cells cultured under normoxic conditions), NC group (IEC-6 cells cultured under hypoxic conditions), HK group (IEC-6 cells transfected with recombinant adenovirus expressing both HIF-1α and KGF under hypoxia), Emodin group (IEC-6 cells were cultured with 5 μmol/L emodin medium under hypoxia conditions) and HKE group (IEC-6 cells expressing both HIF-1α and KGF were cultured with 5 μmol/L emodin medium under hypoxic conditions). After 24 hours of cell culture, the proliferation of IEC-6 cells in each group was detected by MTT method. The DNA content of cells in each group was detected by flow cytometry. The formation of autophagy was observed by scanning electron microscope. The expression of HIF-1α and KGF protein after adenovirus transfection was detected by immunofluorescence staining. The mRNA expressions of beclin-1 and LC3 genes were detected by real time PCR. The protein expressions of beclin-1 and LC3 were detected by Western blot.Results Compared with HK group, Emodin group and HKE group, HKE group could significantly promote the proliferation of IEC-6 cells. The expression of HIF-1α and KGF protein was the highest and the fluorescence intensity was the strongest in HKE group. Compared with BC group, the percentage of cells in G0/G1 phase increased significantly in NC group, and the percentage of cells in G2 and S phase decreased significantly (P＜0.05). The protein expression of beclin-1 and LC3 increased in HK group, Emodin group and HKE group, and the protein and mRNA expression levels of HKE group were significantly higher than those of HK group and Emodin group (P＜0.05). Conclusion Emodin combined with HIF-1α and KGF can protect IEC-6 cells from hypoxia stress through autophagy