Increased demand for highly functional soy protein isolate (SPI) in the food industry draws extra attention to SPI modification. The structural properties and in vitro digestibility of phosphorylated and glycosylated SPI were investigated in this study. The phosphorylation was carried out with sodium tripolyphosphate addition at 45 °C for 4 h. Glucose and dextran were used for glycosylation at 100 °C for 1 h. Apparent molecular weight distribution was determined by size exclusion-high performance liquid chromatography. Thiol content and surface hydrophobicity were also determined. The apparent molecular weight and thiol content of phosphorylated SPI increased with the increase of phosphorylation degree. Meanwhile, phosphorylation negatively affected gastrointestinal digestibility, especially gastric digestibility. The fraction of glycosylated SPI was prone to be low molecular weight, suggesting glycosylation inhibited SPI aggregation, which resulted from the attenuated surface hydrophobicity. The digestibility of SPI was increased by glycosylation. Glucose-based glycosylation contributed to lower intestinal digestion compared with dextran-based glycosylated SPI. This work highlighted that the phosphorylation and glycosylation to SPI primarily affected the in vitro pepsin or pancreatin digestion, inspiring to produce modified SPI with balanced functional and nutritional properties for the food industry.