We predicted the anti-ulcerative colitis (UC) mechanism of Fructus Amomi based on network pharmacology. The anti-UC activity of Fructus Amomi were investigated by in vivo animal experiment, and the active components of Fructus Amomi were obtained through TCMSP, PubChem database and literature research. Animal welfare and experimental procedures follow the regulations of the Animal Ethics Committee of Institute of Materia Medica of Chinese Academy of Medical Sciences. The potential targets of the active components and UC were predicted by SwissTargetPrediction, GeneCards and TTD databases. The protein-protein interaction (PPI) network was constructed by String database and Cytoscape software was used to construct a visual network of active component-disease target and perform topological analysis. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed using Metascape platform. The molecular docking of key components and core targets was carried out by Sybyl X software. We screened out a total of 12 active components and 189 disease-component overlapping targets. Enrichment analyses obtained 227 related GO items and 168 signaling pathways. According to the results of molecular docking, most active components of Fructus Amomi showed good affinity with the JAKs receptor family. Furthermore, Western blot results verified that Fructus Amomi could effectively inhibit JAK/STAT signaling pathway, indicating that Fructus Amomi might exert the anti-UC activity by regulating JAK/STAT signaling pathway.