The effects of washing, soaking, and common domestic cooking methods (normal cooking, high‐pressure cooking, and microwave cooking) on protein content, in vitro protein digestibility, and amino acid composition of japonica and indica rice were investigated. All processes in rice domestic cooking did not affect protein content. However, the gastric and gastrointestinal protein digestibilities decreased significantly after cooking. Protein solubility methods were used to observe the formation of disulfide bonds and hydrophobicity interactions after cooking. Disulfide bonds and hydrophobicity interactions were formed during cooking, and the cooking‐induced disulfide bond cross‐linking decreased the protein digestibility observably. Moreover, the solubility of 13 kDa prolamin subunit sharply decreased after cooking due to intramolecular disulfide bond cross‐linking. Therefore, cooking‐induced formation of intramolecular disulfide linkages might stabilize and strengthen the structure of protein body‐I, which exhibited strong resistance to proteases, particularly pepsin. Cooking had limited effect on amino acids.