In this study, we analyzed the diffusion behavior of additives, such as Cl − and bis-(3-sulfopropyl) disulfide (SPS), during the throughsilicon via process with our surface-enhanced Raman spectroscopy (SERS) measurement system equipped with a model structure of a micro via. The via structure, made of poly(dimethyl siloxane) (PDMS), which has a transparent wall, was attached horizontally on the Cu nano-patterned substrate, an array of nanodots with 150-nm diameter and 300-nm pitch. This substrate provides the SERS effect with high uniformity and also works as one of the sidewalls of the via. The simultaneous diffusion of Cl − and SPS into the micro via on the Cu nanodot wall was observed by Raman microspectroscopy. The obtained SERS spectrum clearly indicated the diffusion of these two species. First, Cl − adsorbs on Cu, because it has a larger diffusion coefficient; SPS removes the pre-adsorbed Cl − to dominate the adsorption site of the surface a few minutes later. Pre-adsorbed SPS is sufficiently stable, and is not removed by a highly negative potential (for example, −200 mV vs. Ag/AgCl).