Objective To explore the mechanism of Gegen Qinlian Decoction in the treatment of ulcerative colitis by network pharmacology and molecular docking. Methods The components and targets of Gegen Qinlian Decoction were searched in Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP). The disease targets of ulcerative colitis in the databases of DrugBank, DisGeNET and TTD were collected. PubChem, Chem3D and PyMOL were used to construct the docking ligands, Autodock was used to process the receptor protein, and CMD vina was used for molecular docking. DAVID was used for GO enrichment analysis and KEGG pathway analysis. Results Gegen Qinlian Decoction could act on 114 core targets of ulcerative colitis, among which MAPK3, MAPK1, STAT3, FOS, MAPK14 were important targets. Quercetin, kaempferol, wogonin, naringenin, baicalein and licorice chalcone A may be the main active components of Gegen Qinlian Decoction, which may act on Cancer, PI3k-Akt, TNF, HIF-1, MAPK, Toll-like receptor, FoxO, Ras and other signaling pathways, so as to play anti-inflammatory, anti oxidative damage, control cell apoptosis, inhibit immunity, and delay tumor progression. Conclusion Gegen Qinlian Decoction may play an anti-inflammatory, anti-oxidation and anti-oxidation role, and delay the progress of tumor through multi-component and multi-target network.