This study was aimed to investigate the effects of phosphorylation and glycosylation on in vitro digestibility of soybean protein. The soybean isolated was phorsphoralated by 2%， 3% and 5% sodium tripolyphosphate， and glycosylated by glucose and dextran respectively. The properties of in vitro gastrointestinal hydrolysates were detected by size exclusion chromatography， ion exchange chromatography as well as Caco-2 monolayer cell model. Charge status， hydrophobicity of the hydrolysates and amino acid composition before and after being transported by Caco-2 monolayer were evaluated. The results showed that phsphoylation and glycosylation changed characteristics of the soybean hydrolysates. Phorsphorlation reduced the molecular weight and neutral peptide content but improved surface hydrophobicity of the hydrolysates. Glucose glycosylated soybean hydrolysates were shown lower molecular weight distribution， surface hydrophobicity and neutral peptide content. Dextran glycosylated soybean hydrolysates were also presented with lower molecular weight distribution and surface hydrophobicity， while the neutral peptide content increased. Phosphorylation and glycosylation decreased the amount of total amino acids， essential amino acids and restricted amino acids （Methionine and Cysteine）. However， with the combined effects of molecular weight distribution， charge status， surface hydrophobicity of the digestive peptides， the loss of amino acid caused by phosphorylation and glycosylation was reduced after being transported by Caco-2 monolayer.