Based on experimental zinc blende and wurtzite models of CdSe nanocrystals, four clusters of CdSe, seven Se-Cd-ligand structures, and their characters are studied at DFT/B3LYP/Lanl2dz theoretical level. Cd(3)Se(3), (Cd(3)Se(3))(2) and (Cd(3)Se(3))(3) clusters which have a ring with six atoms are similar to wurtzite structures, Cd(4)Se(4) have resemblant conformation with zinc blende for they are all composed of tetrahedron. Calculated Raman spectra of Cd(3)Se(3), Cd(4)Se(4), (Cd(3)Se(3))(2) and (Cd(3)Se(3))(3) are about 175 cm(-1) which is consistent with the experimental result. Then, through investigation of Se-Cd-ligand clusters, we find that all Se-Cd-ligand structures have similar characters because main influence of ligands on nanocrystals comes from thiol. Finally, we testify that both solvent and ligand make absorption peaks shift to blue, compared with those in gas phase and without ligand. Under these conditions, calculated data of four clusters are almost identical with the absorption peaks of CdSe nanocrystals. Besides, we also prove that the absorption peaks of four clusters are the transitions from HOMO to LUMO or from d to p orbitals. And HOMO-LUMO gaps reduce in order of Cd(3)Se(3), (Cd(3)Se(3))(2) and (Cd(3)Se(3))(3), which is induced by the quantum size effect.