Functional gastrointestinal disorders (FGIDs) refer to a group of diseases characterized by a series of gastrointestinal symptoms without apparent organic lesions, leading to pathological changes in areas such as the oropharynx, stomach, intestines, anus, and biliary tract. In recent years, the incidence of FGIDs has been increasing annually, with over 40% prevalence globally. However, there is currently no unified standard for treatment both domestically and internationally. This paper defines “Qi” as the spleen-stomach “qi” in traditional Chinese medicine (TCM), where the spleen governs transformation and transportation, and the stomach governs reception and digestion, working together to digest food and absorb nutrients, akin to the gastrointestinal digestive and absorptive functions in Western medicine. “Acid” refers to gastric acid, and “bacteria” denotes the gastrointestinal microbiota. Through modern pharmacological research on TCM herbs combined with traditional TCM concepts, the regulation of gastric acid and gastrointestinal microbiota using relevant herbs has shown efficacy in controlling FGIDs. This paper summarizes and analyzes the “Qi, Acid, Bacteria” theory and provides clinical case examples to demonstrate its effectiveness, suggesting that this approach can offer new insights into the clinical treatment of FGIDs.