Persistent spectral hole burning was widely applied to site-selective spectroscopy of quantum dots (QDs). Size-dependent spherical and torsional acoustic phonon modes confined in CuCl QDs, four size-dependent excited electron-hole quantum states in CdTe QDs, and excited exciton quantum states of (2, 1, 1), (2, 2, 1) and (2, 2, 2) in CuCl quantum cubes were revealed by studying sideband holes.