Molybdenum disulfide (MoS2), a promising two-dimensional transition-metal dichalcogenide, presents a challenge in the tuning of its optoelectronic and chemical properties. Herein, we demonstrate an efficient route to alter the crystalline structure of MoS2 by chemical exfoliation. Using NaK metal alloys, exfoliated and covalently functionalized MoS2 derivatives were obtained with a high metallic (1T) phase ratio, up to 94.5%. Consequently, exfoliated MoS2 showed a significant surface-enhanced Raman scattering activity toward rhodamine 6G (R6G) and crystal violet, with low detection limits. The versatility of this approach allows the covalent functionalization of MoS2 without relying on edge or basal-plane defects of the structure and preserving the high-ratio 1T phase.