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In this experiment, the effect of replacing milk fat with soybean fat body (25%, 50%, 75%, 100%) on the quality, antioxidant capacity and in vitro digestive characteristics of yogurt was investigated while maintaining the total fat content of the yogurt unchanged. The results showed that increasing the substitution amount of soy fat body for milk fat had little effect on the pH and acidity of yogurt during the storage period, while the physicochemical properties, degree of protein gel network crosslinking, saturated fatty acid content, PV value and TBARS value of the yogurt significantly decreased (p < 0.05). Meanwhile, protein content, solids content, unsaturated fatty acid content, tocopherol content and water holding capacity significantly increased (p < 0.05). Flavor analysis revealed that yogurts with soybean oil bodies were significantly different when compared to those without soybean oil bodies (p < 0.05), and yogurt with 25% substitution had the highest sensory score. After in vitro digestion, the free fatty acid release, antioxidant capacity and protein digestibility of soybean oil body yogurt were significantly higher (p < 0.05). The SDS-PAGE results showed that the protein hydrolysis of the soybean oil body yogurt was faster. Therefore, the use of an appropriate amount of soybean oil bodies to replace milk fat is able to enhance the taste of yogurt and improve the quality of the yogurt.