Hierarchical Cu nanoparticles/rGO (CuNPs/rGO) composites were synthesized through the kinetic reaction mediated by hydrophobic methyl trioctyl ammonium chloride (A336) and 2-hydroxy-5-nonyl-acetophenone oxime (LIX84I). The CuNPs/rGO composites were characterized by scanning electron microscopy (SEM), transmission electron microscope (TEM), and X-ray diffraction (XRD), and used as substrates for surface-enhanced Raman scattering (SERS) measurements. The hierarchical CuNPs/rGO composites formed with A336 were assemblies of Cu nanosubunits with a crystal size of 5–10 nm and some observable pinholes, whereas compact Cu nanospheres and nanorods on rGO sheets were formed with LIX84I. Therefore, a hydrophobic ligand-mediated kinetic mechanism was proposed. A synergetic effect on SERS performance was observed for CuNPs/rGO composites and the ratio between CuNPs and rGO was optimized. Moreover, the SERS activity of CuNPs/rGO-A336 was much stronger than CuNPs/rGO-LIX84I owing to the hierarchical structure of CuNPs/rGO-A336. For the CuNPs/rGO-A336 substrate, the detection limit reached 10⁻⁸ mol L⁻¹ for R6G molecules, and quantitative SERS analysis was achieved. The CuNPs/rGO-A336 substrate showed good reproducibility and a high enhancement factor of 2.75 × 10⁶, which is superior to other Cu-based substrates in the literature.