Two amphiphilic catalysts (i.e., metal dodecylbenzenesulfonates, noted as C12BSNi and C12BSFe) were synthesized and characterized by Fourier transform infrared spectroscopy (FT-IR), element analysis (EA), atomic absorption spectroscopy (AAS), and thermogravimetric (TGA). Their interfacial activities were determined using a surface tensiometer and an interfacial tensiometer. Both catalysts are interfacial active and thermostable enough for heavy oil aquathermolysis. Their performance on heavy oil aquathermolysis was assessed in an autoclave. According to the viscosity reduction results, the synthesized amphiphilic catalysts are more effective than water-soluble or oil-soluble catalysts, with C12BSNi more efficient than C12BSFe. The average molecular weight, group compositions, and average molecular structure of heavy oil samples were analyzed using EA, FT-IR, and H-1 nuclear magnetic resonance (1H NMR) before and after aquathermolysis reaction. And the results show that both catalysts caused the change of molecular structures in heavy oil. The change of asphaltene and resin molecular structures and decrease of their contents are crucially important to the reduction of viscosity. C12BSNi causes more changes of the asphaltene than C12BSFe, whereas C12BSFe is beneficial to the breakage of CS bonds in asphlatenes and resins.