Through-silicon-via (TSV) technology enables 3D integration of multiple 2D components in advanced microchip architectures. Key in the TSV fabrication is an additive-assisted Cu electroplating process in which the additives employed may get embedded in the TSV body. This incorporation negatively influences the reliability and durability of the Cu interconnects. Here, we present a novel approach toward the chemical analysis of TSVs which is based on femtosecond laser ablation ionization mass spectrometry (fs-LIMS). The conditions for LIMS depth profiling were identified by a systematic variation of the laser pulse energy and the number of laser shots applied. In this contribution, new aspects are addressed related to the analysis of highly heterogeneous specimens having dimensions in the range of the probing beam itself. Particularly challenging were the different chemical and physical properties of which the target specimens were composed. Depth profiling of the TSVs along their main axis (approach 1) revealed a gradient in the carbon (C) content. These differences in the C concentration inside the TSVs could be confirmed and quantified by LIMS analyses of cross-sectionally sliced TSVs (approach 2). Our quantitative analysis revealed a C content that is ∼1.5 times higher at the TSV top surface compared to its bottom. Complementary Scanning Auger Microscopy (SAM) data confirmed a preferential embedment of suppressor additives at the side walls of the TSV. These results demonstrate that the TSV filling concept significantly deviates from common Damascene electroplating processes and will therefore contribute to a more comprehensive, mechanistic understanding of the underlying mechanisms.