The importance of phonons and their interactions in bulk materials is well known to those working in the fields of solid‐state physics, solid‐state electronics, optoelectronics, heat transport, quantum electronic, and superconductivity. Phonons in nanostructures may act as a guide to research on dimensionally confined phonons and lead to phonon effects in nanostructures and phonon engineering. In this chapter, we introduce phonons in zinc blende and wurtzite nanocrystals. First, the basic structure of zinc blende and wurtzite is described. Then, phase transformation between zinc blende and wurtzite is presented. The linear chain model of a one‐dimensional diatomic crystal and macroscopic models are also discussed. Basic properties of phonons in wurtzite structure will be considered as well as Raman mode in zinc blende and wurtzite structure. Finally, phonons in ZnSe, Ge, SnS2, MoS2, and Cu2ZnSnS4 nanocrystals are discussed on the basis of the above theory.