Understanding the size-dependent structures and properties of ligand-capped nanoclusters in solvent is of particular interest for the design, synthesis and application of II–VI colloidal QDs. Using DFT and TDDFT calculations, we studied the structure and optical property evolution of the cysteine-capped (CdSe)_N clusters of N = 1–10, 13, 16 and 19 in gas, toluene, water and alkaline aqueous solution, and made a comparison with their corresponding bare clusters. The cysteine binds with (CdSe)_Nvia several patterns depending on the medium they exist in, affecting the cluster structures and in consequence their optical absorption. In general, the absorption bands of (CdSe)_N blueshift when cysteine is added, and the shift varies with the interaction strength between the cluster and the ligand, and the dielectric constant of the solvent. However, bare clusters retain their size sensitivity, in particular the redshift trend with increasing cluster size, and some similarity was noted for the optical absorption of the bare and ligated clusters regardless of the gas or solvent media. Population analysis reveals that the excitations are mainly from orbitals distributing on the (CdSe)_N part, while the ligand is negligibly involved in the excitations. This is an important feature for the II–VI QDs as biosensors with which the information of biomolecules is detected from the size dependent optical absorption or emission of the QDs other than the biomolecules.