Multilayer hyperbolic metamaterial (HMM)-based SERS substrates have received special consideration because they accommodate various propagation modes such as surface plasmonic polaritons (SPP). However, the SPP modes are difficult to generate in HMM due to their weak electric field enhancement. In this article, we designed novel SERS substrates consisting of graphene-covered AgNPs and HMM. The graphene-covered AgNPs work as an external coupling structure for hyperbolic metamaterials due to this structure exhibiting significant plasmonic effects as well as unique optical features. The localized surface plasmonic resonance (LSPR) of the graphene-covered AgNPs excited the SPP and thus formed a strong hot spot zone in the nanogap area of the graphene. The Raman experiment was performed using rhodamine 6G (R6G) and crystal violet (CV), which showed high stability and a maximum enhancement factor of 2.12 × 108. The COMSOL simulation further clarified that enhanced SERS performance was due to the presence of monolayer graphene and provided an atomically flat surface for organic molecules in a more controllable manner. Interestingly, the proposed SERS structure carries out quantitative detection of thiram in soil and can satisfy the basic environmental need for pesticide residue in the soil.