Salt stress is a critical abiotic constraint affecting wheat yield and quality. In this study, we employed pot experiments under controlled salinity (2.8‰ NaCl) and multi-omics approaches to elucidate the regulatory mechanisms underlying grain quality formation in a strong-gluten wheat variety, Jinan 17. Key findings revealed that salt stress caused a significant 41.27% reduction in 1000-kernel weight, while protein content increased by 13.82%. However, bread volume and bread score were reduced by 16.85% and 13.08%, respectively. Multi-omics integration uncovered that salt stress repressed the expression of starch synthesis-related genes (e.g., TraesCS2A03G0349200), diverting carbon skeletons toward amino acid metabolism pathways. This metabolic reprogramming disrupted the glutenin/gliadin ratio (down 14.35%), with high molecular weight glutenin subunits (HMW-GS) synthesis being suppressed, while low molecular weight glutenin subunits (LMW-GS) and gliadin accumulated by 19.28% and 24.76%, respectively, forming a “high extensibility but low elasticity” gluten network. Furthermore, transcriptomic analysis identified significant upregulation of arginine metabolism genes (e.g., TraesCS6A03G0029900), which enhanced osmolyte biosynthesis and exacerbated carbon–nitrogen partitioning imbalances. This study provides novel insights into the molecular mechanisms of flour quality deterioration under saline conditions and identifies critical regulatory nodes for simultaneous improvement of starch synthesis and gluten network architecture in salt-affected wheat breeding programs.