Gegen Qinlian Decoction(GQD) is commonly used for the clinical treatment of ulcerative colitis(UC) and other diseases, but its compatibility mechanism has not been elucidated systematically. In this study, the compatibility mechanism of GQD against UC was revealed based on the blood components in the mouse model of UC by network pharmacology. The targets of blood components of GQD were collected to construct a protein-protein interaction(PPI) network. The key targets were screened out according to the topological parameters of the network, and 16 core components were identified, such as puerarin, chrysin, berberine, and liquiritigenin, based on the key targets in the blood components. Functional enrichment analysis was performed on the key targets, and the regulatory network of the prescription was constructed, which elucidated the compatibility mechanism of the Chinese herbal drugs in the prescription at both target and pathway levels. The results showed that all the Chinese herbal drugs in GQD had heat-clearing and toxin-removing effects, and the four Chinese herbal drugs synergistically exerted their effects by co-regulating protooncogenes, such as FOS and JUN, and characteristically regulating signal transducer and activator of transcription 3(STAT3) and interleukin-6(IL-6). The pathway analysis revealed that GQD exerted heat-clearing and toxin-removing effects mainly by regulating the inflammatory response-related signaling pathways, such as Toll-like receptor, tumor necrosis factor(TNF), and mitogen-activated protein kinase(MAPK). Furthermore, the study revealed the synergistic effects of Chinese herbal drugs in GQD based on the TNF signaling pathway. The results showed that the sovereign drug Puerariae Lobatae Radix played a primary role in the regulation of targets in the TNF signaling pathway, the minister drugs Scutellariae Radix and Coptidis Rhizoma showed the synergistic effects with Puerariae Lobatae Radix, and the assistant and guiding drug Glycyrrhizae Radix et Rhizoma supported Puerariae Lobatae Radix in the key target NF-κB and the process of cell adhesion. The drugs in GQD showed good characteristics of compatibility in the TNF signaling pathway. This study is expected to provide the basis for the further exploration of the compatibility mechanism of GQD.