This study used dual-frequency countercurrent probe ultrasound (DFU) to prepare sodium caseinate (Cas)-Pectin (Pec) complex-stabilized emulsion. Besides analyzing the physicochemical properties and structural characteristics, the current study assessed the impact of DFU on the encapsulation efficiency (EE), bioavailability, antioxidant activity, and stability of quercetin (QUE)-loaded emulsions. The results indicated that DFU (20/28 kHz) improved the emulsion resistance to environmental stress by increasing the interaction between the lipid-complex and decreasing the droplet size (from 12.60 to 3.09 μm), mainly manifesting the higher stability index (improved to 97%). Furthermore, DFU enhanced the interface Cas/Pec adsorption than high-speed shear homogenization (improved from 3.55 to 6.29 mg/m2 for Cas and from 3.28 to 5.83 mg/m2 for Pec) and exhibited better uniformity. The aforementioned enhancements exhibited a positive impact on emulsion loading QUE, improving its EE (from 69 to 83%) and increasing its bioavailability (from 12% to 48%). Furthermore, emulsion stability was improved through the reduction of free radical production and QUE degradation induced by environmental factors.