Ligand molecules capping on clusters largely affect the formation and stabilization mechanism and the property of clusters. In semiconductor CdSe clusters, cysteine is used as one of the ligands and allows the formation of ultrastable (CdSe)34 magic-sized clusters. Cysteine has sulfhydryl, amine, and carboxylate groups, all of which have coordination ability to the CdSe surface, and the bonding states of the three functional groups of ligand–cysteine on the CdSe core have not been determined. In this work, the capping structure of ligand–cysteine is examined by performing Fourier transform infrared (FT-IR) spectroscopy, X-ray photoelectron spectroscopy (XPS), and multinuclear solid-state nuclear magnetic resonance (NMR) spectroscopy. FT-IR, XPS, and 1H, 13C, and 23Na magic-angle spinning NMR show that the sulfhydryl group of ligand–cysteine forms a sulfur–cadmium bond with a cadmium atom at the CdSe surface, while the carboxylate group does not contribute to the protection of the CdSe core and binds to a sodium ion contained as a counterion. 15N–{77Se} through-bond J-single quantum filtered NMR experiment reveals that the amine group of ligand–cysteine has no coordination to selenium atoms. By considering the N–Cd bond forming ratio (∼43%) revealed in our previous work, which is confirmed in this work by analyzing 13Cα signal intensity (∼42%), we concluded that cysteine capping on (CdSe)34 occurs in two ways: one involves both the sulfur–cadmium and nitrogen–cadmium bonds, and the other bears only the sulfur–cadmium bond.