Surface-enhanced Raman scattering (SERS) has been widely used in food and drug detection, biological and medical sensing. In recent years, the study of non-metallic SERS substrates has gradually become a hot field of SERS. Here, we investigated the modulation effects on SERS activities of 2,3,5,6-tetrafluoro-7,7,8,8-tetrachyanoquindimethylene (F<sub>4</sub>TCNQ) grown on molybdenum disulfide (MoS<sub>2</sub>) films. The different nanostructures of F<sub>4</sub>TCNQ can have an effect on the bound ability of charges transferred from the surface of MoS<sub>2</sub>, which changes the electron density distribution on the surface of the F<sub>4</sub>TCNQ/MoS<sub>2</sub> nanocomposite material. Therefore, the interface exhibited different charge localization in the F<sub>4</sub>TCNQ/MoS<sub>2</sub> nanocomposite. The charge transfer efficiency between the substrate and with the adsorbed probe molecules leads the substrate to show a different SERS sensitivity. The enhancement factor of 4-mercaptobenzoic acid (4-MBA) molecules on the most optimized 7-min F<sub>4</sub>TCNQ/MoS<sub>2</sub> nanocomposite substrate can reach 6.9×10<sup>4</sup>, and the detection limit concentration is as low as 10<sup>-6</sup>M. The results of research on F<sub>4</sub>TCNQ/MoS<sub>2</sub> nanocomposite provides an effective optimization scheme of energy level regulation for SERS based on the chemical enhancement mechanism, and opens up a new way to further exploit its functional applications.