Abstract: Germination, as a natural bioprocessing technique, has been demonstrated to effectively enrich bioactive components in wheat, such as γ-aminobutyric acid (GABA), polyphenols, and arabinoxylan, while simultaneously modifying the structural and physicochemical properties of wheat starch. These modifications significantly enhanced the bioavailability and nutritional quality of wheat-based products. To optimize germination conditions, this study employed a synergistic strategy combining ultrasonic pretreatment with NaCl-induced salt stress. Wheat grains were treated with a 60 mmol/L NaCl solution under varying germination durations (24, 48, and 72 h) following ultrasonic processing. Starch was subsequently extracted from germinated wheat through homogenization, and its characteristics were systematically compared among three groups: the blank group (non-germinated), NaCl treatment group (ultrasonic combined with NaCl), and control group (ultrasonic only). The results indicated that the optimal condition for improving starch functionality was ultrasonic-assisted NaCl treatment for 48 h. NaCl stress significantly affected starch properties, including surface morphology, particle size distribution, crystalline structure, and degree of branching. Specifically, after 48 hours of ultrasonic treatment combined with NaCl, the functional properties of starch reached the best level: the phenolic content reached a peak of 1.50 mg gallic acid equivalents/g dry weight; the starch particle size increased substantially, indicating structural loosening; the lamellar structure was destroyed; the fractal dimension decreased from 2.25 to 1.96, indicating increased internal disorder and reduced molecular compactness. Rheological analysis demonstrated a notable decline in peak viscosity (2 098.50 mPa·s vs. 2 450 mPa·s in controls), suggesting weakened starch granule integrity. Conversely, differential scanning calorimetry (DSC) indicated an elevated gelatinization enthalpy (11.25 J/g), attributed to modified amylopectin double-helix alignment. These multi-scale modifications in starch structure-function relationships highlight the synergistic potential of ultrasonic and NaCl treatments in modulating germination dynamics. The optimized protocol not only enhances the synthesis of bioactive compounds but also tailors starch properties for specific food applications, such as low-viscosity or high-digestibility formulations, thereby promoting the development of nutritionally fortified wheat-based products. In conclusion, 48 hours of NaCl-ultrasound combined treatment is the optimal condition, and the corresponding starch has good thermal stability, low viscosity, and high solubility. This study provides experimental evidence for further investigating the structural and functional changes of starch in sprouted wheat under salt stress.