Two-dimensional (2D) molybdenum disulfide (MoS2) holds great promise in electronic and optoelectronic applications owing to its unique structure and intriguing properties. The intrinsic defects such as sulfur vacancies (SVs) of MoS2 nanosheets are found to be detrimental to the device efficiency. To mitigate this problem, functionalization of 2D MoS2 using thiols has emerged as one of the key strategies for engineering defects. Herein, we demonstrate an approach to controllably engineer the SVs of chemically exfoliated MoS2 nanosheets using a series of substituted thiophenols in solution. The degree of functionalization can be tuned by varying the electron-withdrawing strength of substituents in thiophenols. We find that the intensity of 2LA(M) peak normalized to A1g peak strongly correlates to the degree of functionalization. Our results provide a spectroscopic indicator to monitor and quantify the defect engineering process. This method of MoS2 defect functionalization in solution also benefits the further exploration of defect-free MoS2 for a wide range of applications.