Heat-denatured wheat gluten (HDWG) degradation during freeze-thaw (FT) cycling is a key factor in the quality deterioration of pre-cooked noodles (PCNs). This study investigated the effects and underlying mechanisms of sodium chloride (NaCl) on HDWG. Adding NaCl enhanced the luminance of PCNs and reduced chromatic aberration. Scanning electron microscopy revealed that NaCl facilitated a more continuous microstructure, resulting in a reduction the average hole size of HDWG from 84.44 μm to 56.59 μm after 10 FT cycles. With the FT cycling, gluten macropolymer (GMP) depolymerization occurs, causing the collapse of HDWG network structure. However, NaCl contributed to the formation of β-sheet and gauche-gauche-gauche (g-g-g) conformations, resulting in a stronger three-dimensional structure of HDWG, thus alleviating GMP depolymerization. The analysis of intermolecular interactions shows that NaCl primarily affects hydrogen bonds, disulfide bonds, and hydrophobic interactions, and stabilizes the structural integrity of HDWG by balancing these forces. NaCl altered the three-dimensional structural composition of HDWG by influencing the intermolecular interactions, thereby fortifying the PCNs against FT cycling. This study provides a robust theoretical basis for using NaCl to regulate the quality of thermally precooked flour products.