Microscopic phonon theory of semiconductor nanocrystals (NCs) is reviewed in this paper. Phonon modes of Si and Ge NCs with various sizes of up to 7 nm are investigated by valence force field theory. Phonon modes in spherical SiGe alloy NCs approximately 3.6 nm (containing 1147 atoms) in size have been investigated as a function of the Si concentration. Phonon density-of-states, quantum confinement effects, as well as Raman intensities are discussed.