Soybean protein is widely used in food processing as raw materials, at the same time is a good source of amino acids that can be ingested by human beings. In order to improve the functional properties of soy protein in industrial production, the modifications are usually made, causing the low amino acid digestion and absorption. This review summarized the functional properties and nutritional value of soybean protein, the main modification and its influence on amino acid availability, and the present researches of soybean protein, put forward some suggestions and research directions in the future, and comprehensively presented the amino acid inefficient problem of soy protein resulted from modifications. This study also explained the relationship between the protein aggregates and the amino acid digestibility, and provided some suggestions about improving the utilization rate of soybean protein and innovation of production.