Wastewater contains various high-risk trace organic pollutants, such as antibiotics and endocrine disruptors, which seriously restrict wastewater reuse. Cyclodextrin-based functional materials show great potential in the removal of trace pollutants because of their adsorption catalytic synergy. Clarifying the synergistic mechanism of cyclodextrin in oxidation is the key issue in confined catalytic oxidation process design. In this work, we fabricated a BiOIO3@BiOBr/β-CD heterojunction photocatalyst to study the synergistic mechanism of cyclodextrin in the photocatalytic oxidation process. The synergistic mechanism of cyclodextrin was investigated by combining radical chemistry, electrochemistry, spectroscopy, and time-dependent density functional theory. Results showed that the excited intermediate free radicals played an important role in promoting the photocatalytic degradation process. The heterojunction photocatalyst loaded with β-cyclodextrin (β-CD) at the electronic end (C[Cat.] = 0.2 mg/mL) removed about 97% of bisphenol A (BPA) within 30 min, and the first-order kinetic constant (kCDBIB = 0.112 min−1) was about twice that of the unloaded β-CD (kBIB = 0.057 min−1). Cyclodextrin loading improved the photocatalytic performance of the heterojunction and stimulated the intermediate to increase the free radical yield and regulate the reaction path.