Soymilk is a natural nanocarrier. However, the performance of flavonoid-soymilk nano-complex remains unclear. In this work, icariin-soymilk nano-complexes (ISNCs) were successfully fabricated and characterized. The effects of high-pressure homogenization (HPH) treatment on structure and physicochemical properties of soymilk and nano-complexes were investigated. HPH treatment could significantly improve the surface hydrophobicity and interfacial activity of soymilk. The soymilk with HPH treatment could significantly improve the water solubility (20 folds), thermal stability and bioavailability of icariin. The highest encapsulation efficiency (93.28%), loading capacity (39.09 μg/mg), ζ-potentia (absolute value, 31.20 mV) and bioavailability (72.14%) were observed in HSI-200 (200 bar of homogenization pressure). While HSI-500 (500 bar of homogenization pressure) showed the smallest particle size (183.73 nm). ISNCs showed a rougher surface and an irregular lamellar structure with large amount of fine particles by using Cryo-SEM, suggesting that icariin was encapsulated in soymilk. These data supplied a novel strategy to improve the performance of icariin in functional foods.