Despite the significant progress, the controlled deposition of nanoparticles onto the support materials having 3-D nano-morphologies is still facing challenges due to the limited diffusion of metal ions into the nanostructures and uncontrolled aggregation of nanoparticles. In this study, a simple yet versatile alternative is demonstrated to control the silver nanoparticle (AgNP) density and morphology onto the 3-D silicon nanowire (SiNW) arrays based on bio-inspired polydopamine (PDOP) coating and electroless plating approaches for practical Surface-Enhanced Raman Spectroscopy (SERS) applications. In order to control silver deposition and its morphology and to optimize the SERS performance of AgNP decorated SiNW arrays, the effect of some key experimental parameters including SiNW length and morphology, silver reduction time and PDOP thickness are investigated in detail. The optimized samples demonstrate remarkable surface-enhancement ability in Raman signals with high reproducibility (lower than 10% spot-to-spot and sample-to-sample). Interestingly, it is found that PDOP coating not only serves as a reducing agent for the deposition of AgNPs on SiNW arrays in a controlled manner, but also contributes to the observed SERS enhancements in terms of improving photon scattering and promoting electron transfer processes due to its organic semiconductor nature.