Data mining, network pharmacology, and molecular docking methods were employed to elucidate the compatibility patterns and mechanisms of action of nationally authorized patented Chinese herbal compound formulas in the treatment of GERD (gastroesophageal reflux disease). Chinese herbal patent formulas for GERD treatment were retrieved from the National Intellectual Property Administration patent database. Frequency statistics, association rule mining, and systematic cluster analysis were performed using Excel 2021, SPSS Statistics 26.0, and SPSS Modeler 18.0 to summarize medication characteristics and identify core herb combinations. Network pharmacology was then applied to explore the active ingredients and targets of the core herb combination in GERD treatment, followed by molecular docking to verify binding activity. A total of 143 patented Chinese herbal formulas for GERD were included, involving 238 Chinese herbs. High-frequency herbs were mainly tonifying herbs, qi-regulating herbs, and heat-clearing herbs. The top seven herbs were Gancao, Huanglian, Banxia, Chaihu, Haipiaoxiao, Wuzhuyu, and Chenpi. The herb properties were predominantly cold, with bitter, pungent, and sweet flavors dominating, mainly associated with the spleen, stomach, lung, and liver meridians. Association rules identified herb combinations such as Wuzhuyu-Chaihu-Huanglian-Zhiqiao, Zhiqiao-Huanglian-Wuzhuyu, and Daizheshi-Zhiqiao-Chaihu. Cluster analysis yielded six new clusters, including Huanglian-Wuzhuyu-Chaihu-Zhiqiao-Daizheshi-Banxia-Haipiaoxiao-Gancao-Chenpi and Houpo-Walengzi. The combination Wuzhuyu-Chaihu-Huanglian-Zhiqiao was determined as the core herb combination. Network pharmacology revealed that this combination contains active ingredients such as quercetin, berberine, and obacunone, acting on key targets including HIF1A, TNF, and BCL2, and modulating pathways such as IL-17 signaling and Th17 cell differentiation. Molecular docking confirmed that obacunone (MOL013352) exhibited the optimal binding energy with MTOR. Patented Chinese herbal formulas for GERD follow the principles of tonifying deficiency, regulating qi, clearing heat, and inhibiting acid. The core herb combination Wuzhuyu-Chaihu-Huanglian-Zhiqiao exerts therapeutic effects by targeting MTOR and other key proteins and regulating signaling pathways such as IL-17 and Th17 cell differentiation.