Extruded glutelin/rice starch composites were prepared using twin-screw extrusion at various specific mechanical energies (SME), and the interaction mechanism of glutelin and rice starch was investigated at the molecular level. The results indicated that the structure of glutelin was destroyed, hydrophobic interactions and hydrogen bonds between rice starch and glutelin were formed and enhanced as the SME increased, and new hydrogen bonds were formed at the carbonyl (δ- and γ-carbons of glutelin) and C-1 of Tyr. Molecular docking studies confirmed that SME promoted the simultaneous occurrence of the Millard reaction and non-covalent reaction between glutelin and small molecular sugars produced by starch degradation, providing information on binding sites. Additionally, scanning electron microscopy (SEM) revealed dense and uniform flake-like structures induced by these binding interactions. Overall, insights into the interaction mechanism of rice starch and glutelin provide theoretical references for generating reconstituted rice products using extrusion processing.