Based on previous research suggesting that milk exosomes specifically express miR-26a, this study optimized the miR-26a encapsulation efficiency of liposomes through ultrasonic treatment, and it also evaluated the in vitro digestion performance of the ultrasonic-treated liposomes and compared its anti-inflammatory activity with that of natural milk exosomes. Single-factor experiments were conducted to optimize the molar charge ratio of cationic liposome vector to nucleic acid (N/P), ultrasonication time, and ultrasonic power for the preparation of miR-26a-encapsulated liposomes. The results demonstrated that when the N/P ratio was 4, ultrasonication time was 15 min, and ultrasonic power was 300 W, the encapsulation efficiency reached its peak of (89.51 ± 1.37)%, with uniform particle size distribution and homogeneous morphology. In vitro simulated digestion experiments showed that the retention rate of miR-26a in the ultrasonic-treated liposomes (58%) was higher than that in the conventional liposomes (24%). Cell function experiments confirmed that the ultrasonic-treated liposomes not only enhanced the viability of normal Caco-2 cells but also effectively inhibited lipopolysaccharide (LPS)-induced inflammatory responses, significantly restoring cell viability under inflammatory conditions. Additionally, it reduced NO release and down-regulated the secretion of the inflammatory cytokines interleukin 6 (IL-6), tumor necrosis factor α, and IL-1β, while effectively controlling the generation of reactive oxygen species. Notably, the ultrasonic-treated liposomes showed no significant differences from milk exosomes in terms of cell viability regulatory and inflammation inhibitory effects. In summary, this study demonstrates that ultrasonic can significantly improve the miR-26a delivery efficiency of liposomes.