Two-dimensional layered material Molybdenum disulfide (MoS2) exhibits a flat surface without dangling bonds and is expected to be a suitable surface-enhanced Raman scattering (SERS) substrate for the detection of organic molecules. However, further fabrication of nanostructures for enhancement of SERS is necessary because of the low detection efficiency of MoS2. In this paper, period-distribution Si/MoS2 core/shell nanopillar (NP) arrays were fabricated for SERS. The MoS2 thin films were formed on the surface of Si NPs by sulfurizing the MoO3 thin films coated on the Si NP arrays. Scanning electron microscopy, Raman spectroscopy, and X-ray photoelectron spectroscopy were performed to characterize Si/MoS2 core-shell nanostructure. In comparison with a bare Si substrate and MoS2 thin film, the use of Si/MoS2 core-shell NP arrays as SERS substrates enhances the intensity of each SERS signal peak for Rhodamine 6G (R6G) molecules, and especially exhibits about 75-fold and 7-fold enhancements in the 1361 cm−1 peak signal, respectively. We suggest that the Si/MoS2 core-shell NP arrays with larger area could absorb more R6G molecules and provide larger interfaces between MoS2 and R6G molecules, leading to higher opportunity of charge transfer process and exciton transitions. Therefore, the Si/MoS2 core/shell NP arrays could effectively enhance SERS signal and serve as excellent SERS substrates in biomedical detection.