Signal enhancement of spectroscopies including terahertz time-domain spectroscopy (THz-TDS) and surface-enhanced Raman scattering (SERS) is a critical issue for effective molecular detection and identification. In this study, the sensing performance between THz-TDS and SERS individually accompanied by the proper plasmonic subwavelength structures was compared. For the precisely quantitative study on the optical properties of rhodamine 6G (R6G) dyes, SERS incorporates with the non-linearly enhanced Raman emissions at the molecular characteristic peaks while THz-TDS refers to the transmittance change and the shift of the spectral resonance. The local molecular density-dependent trade-off relationship between limit-of-detection and quenching was observed from both measurements. The specificity for two samples, R6G and methylene blue, is determined by the discriminations in spectral features such as the intensity ratio of assigned peaks in SERS and transmittance difference in THz-TDS. The comprehension of field enhancement by the specific nanostructures was supported by the finite-element method-based numerical computations. As a result, both spectroscopic techniques with the well-tailored nanostructures show great potential for highly sensitive, reproducible, label-free, and cost-effective diagnosis tools in the biomedical fields.