This work presents the design, synthesis, UV-Vis absorption properties and Cu²⁺ ion binding of the organo-silicon complexes (3a–h) with different coordination abilities that are derived from mercaptopropylsilatrane (MPS) and respective heteroaromatic carboxylic acids (1a–h). The prepared thioester based organosilatranes (ThE-OS) have been meticulously characterized by a series of characterization techniques such as elemental analyses, FT-IR, NMR (¹H, ¹³C), LC-MS, and structure of 3e was unambiguously determined by X-ray single crystal analyses. All the compounds have shown judicious absorption enhancement in the intensity as well as λ_max values on binding with Cu²⁺ ions compared to other surveyed metal ions. In addition, it is for the first time that the hybrid silica nanoparticles (H-SiNPs) bearing a thioester linkage in the silica framework are reported. The synthesis was achieved conveniently by an in situ co-condensation reaction of tetraethyl orthosilicate (TEOS) with the corresponding ThE-OS. The derivatization of silica is confirmed by FT-IR, ¹³C and ²⁹Si solid state CP-MAS NMR, UV-Vis, TEM, XRD, TGA and EDX techniques. Furthermore, the H-SiNPs have exhibited greater affinity towards Cu²⁺ ions than the parent ThE-OS.