The invention provides a siloxane quaternary ammonium salt modified amphiphilic polymer ultra-heavy oil viscosity reducer and a preparation method and an application thereof. Firstly, two kinds of double bond-containing siloxane-based quaternary ammonium salt monomers with different structural features are synthesized, and the viscosity reducer is obtained through radical solution polymerization of the double bond-containing siloxane-based quaternary ammonium salt monomers with cationic monomers and acrylamide respectively. The viscosity reducer is used for ultra-heavy oil and has good viscosity reducing effects, temperature resistance and salt resistance, excellent viscosity reducing effects and the like for high-mineralization ultra-heavy oil. The ultra-heavy oil is easy to be demulsified and dehydrated after being subjected to emulsification and viscosity reduction treatment. The synthetic process of the method is simple and easy to control, the obtained viscosity reducer can be used alone and does not need to be compounded and used together with other additives, and the viscosity reducer is excellent in comprehensive performance, green and environmentally friendly.