In this study, we develop a filter paper-supported Ag nanowire (AgNWs) substrate coated with a tunable layer of zeolitic imidazolate framework-67 (ZIF-67) metal-organic framework (MOF) for surface-enhanced Raman scattering (SERS) applications. The thickness of the ZIF-67 layer is precisely controlled by adjusting the soaking time, allowing us to investigate the influence of MOF thickness on SERS performance using probes with different sizes. Sensitivity for large, impenetrable molecules such as thiram and rhodamine 6G (R6G) are primarily governed by localized surface plasmon resonance (LSPR), while smaller, penetrable molecules like 4-mercaptobenzoic acid (4-MBA) exhibit enhanced sensitivity driven by charge transfer (CT) effects due to their ability to penetrate the MOF layer. A finite-difference time-domain (FDTD) simulation reveals that the porous structure of ZIF-67 facilitates electric field propagation to the probe, maintaining significant LSPR effects even beyond 200 nm from the AgNWs. Practical applicability is demonstrated using a wiping mode to detect thiram spiked on apple surfaces, with reliable linear detection achieved across a wide range of concentrations. This study underscores the potential of MOF-based hybrid SERS substrates for real-world applications, leveraging the complementary roles of CT and electromagnetic (EM) mechanisms to enhance sensitivity.