As consumer demand for low-salt diets increases, the development of low-salt cheese has emerged as a prevailing trend. To gain a deeper insight into the effects of salt reduction on cheddar cheese, this study used cheddar cheese with a 2.0% salt concentration (full salt, FS) as the standard control, exploring the differences in quality and composition between cheddar cheese with a 1.5% salt concentration (reduced salt, RS) and a 1.0% salt concentration (half salt, HS). The results revealed that, while the RS group exhibited significant differences in texture compared to the FS group, their physicochemical composition and microbial communities were similar, resulting in a product with quality comparable to traditional cheese. In contrast, the HS group differed notably from the FS group in terms of its physicochemical composition, texture, and microbial communities. Shifts in the microbial community within the HS group promoted enhanced protein metabolism, producing a substantial increase in free amino acids and volatile flavor compounds. In summary, cheddar cheese with a 1.5% salt concentration is similar to traditional varieties in terms of quality, while the 1.0% salt variety displays a more complex composition, due to microbial community shifts facilitating protein metabolism.