Water is the most sustainable solvent, making it the obvious choice to replace organic solvents in various synthesis techniques. However, its applications in the chemical and pharmaceutical industries are often restricted by the low solubility of organic compounds in water. Essentially, the reactions of organic compounds in water are multiphase systems. Therefore, this review classifies aqueous-phase organic reactions into liquid–liquid, liquid–solid and gas–liquid–solid phase from the perspective of phase interfaces of multiphase reactions, and summarizes the research progress and breakthroughs in recent years, including the application of micellar catalysis, Pickering emulsion catalysis, micro-nanobubble/foam catalysis and “dry water” catalysis, as well as the unique advantages of using water as a medium. Finally, we point out the current challenges and future perspectives on multiphase catalysis in aqueous-phase reactions.