ObjectiveTo predict the targets and signaling pathways of Si Junzitang and Tongxie Yaofang in treating ulcerative colitis （UC） following the concept of "same disease with different treatments" based on the network pharmacology and explore the underlying mechanisms. MethodThe differentially expressed genes （DEGs） of UC were extracted from GeoChip. The active components and corresponding potential targets of Si Junzitang and Tongxie Yaofang were collected from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform（TCMSP）. The regulatory networks of Si Junzitang and Tongxie Yaofang were constructed and the protein-protein interaction （PPI） network was plotted. The core genes were predicted， followed by enrichment analysis. The UC model was induced in mice by dextran sodium sulfate （DSS） solution. Mice were randomly divided into a normal group， a UC group， a Si Junzitang group， a Tongxie Yaofang group， and a mesalazine group. Drugs were administered continuously for 14 days. The disease activity index （DAI） was scored for mice in each group. The characteristic values of hemorheology were measured. The serum levels of interleukin-6 （IL-6）， tissue factor （TF）， and hypoxia-inducible factor-1α （HIF-1α） in mice were detected. The relative mRNA expression levels of inhibitory kappa B kinase α （IKKα）， nuclear factor kappa B （NF-κB）， HIF-1α， and vascular endothelial growth factor （VEGF） were measured. ResultA total of 44 genes were obtained by network pharmacological analysis， including 17 common genes. HIF-1 pathway and hypoxia response were potential common targets of Si Junzitang and Tongxie Yaofang in the treatment of UC. The results showed that Si Junzitang and Tongxie Yaofang could significantly reduce DAI score， increase blood perfusion volume and blood cell movement speed， decrease the concentration of mobile red blood cells， reduce the levels of IL-6， TF， and HIF-1α， down-regulate the mRNA expression of IKKα， NF-κB， HIF-1α， and VEGF. ConclusionThe HIF-1 pathway and related targets may be the common targets of Si Junzitang and Tongxie Yaofang to exert different therapeutic effects on the same disease. Si Junzitang is potent in promoting Qi circulation to improve intestinal tissue hypoxia， and Tongxie Yaofang is effective in promoting blood circulation to facilitate intestinal mucosal microcirculation.