The formation of water-in-oil waxy crude oil emulsions deteriorates the rheological properties of the oil−water mixture. Magnetic treatment technology is an effective method to improve the flowability of a crude oil emulsion. A novel magnetic processing apparatus was developed. An experimental method was proposed for the magnetic treatment of the crude oil emulsion at particular shear rates. The apparent viscosity variation of the emulsion with the magnetic field intensity, magnetic field frequency, and magnetic treatment duration was investigated. When the viscosity measuring temperature is 27 °C, the optimal viscosity reduction effect is 12.48%, occurring at 120 mT, 250 Hz, and 15 min. When the viscosity measurement temperature drops to below the wax appearance temperature, the viscosity reduction rate under the same magnetic treatment conditions is 15.14%. The analysis demonstrates that the magnetic field increases the intermolecular dispersion force between wax molecules. The resulting formation of larger aggregations in the crude oil phase reduces the apparent viscosity of the crude oil phase and emulsion. The changing magnetic field generates an induced electromotive force at the dispersed phase and the oil−water interface film, causing the asphaltene molecules at the interface to oscillate. The interfacial film strength, emulsion stability, and interfacial tension are thus reduced, leading to a tendency for the dispersed phase to coalesce. The emulsion viscosity first decreases and then increases with the increase in field intensity. The emulsion viscosity reduction effect increases with the field frequency, and the reason for this is that a higher frequency promotes the oscillation of asphaltene molecules. The extension of the treatment duration has little contribution to the reduction of emulsion viscosity, and the considered effective treatment duration is 15 min. The research results provide a theoretical basis for the field application of viscosity reduction for water-in-oil waxy crude oil emulsions by magnetic treatment technology.