Germination can enhance the nutritional properties of wheat and improve its bioavailability, while simultaneously altering the microstructure of wheat starch, which further impacts its physicochemical characteristics. This work investigated the synergistic effects of germination and NaCl on the microstructure and physicochemical properties of wheat starch by applying a 60 mmol/L NaCl solution. The results indicated that germination significantly influenced both the chemical composition and microstructure of wheat starch, as evidenced by cracks and pores, variations in size, crystallinity, lamellar order, hydrogen bond disruption, branching degree, and molecular weight distribution. These changes affected the pasting and gel properties of the starch. The NaCl treatment enhanced enzyme activity, resulting in a higher phenolic content (4.70 mg GAE/g DW) at 48 h, rougher and irregular surfaces, smaller dimensions (D