We describe a model for numerical calculation of phonon spectrum in a three-dimensional regimented array of semiconductor quantum dots. Regimentation and possibility of carrier mini-band formation make this structure analogous to a crystal, e.g.quantum dot crystal. It is demonstrated that the acoustic phonon dispersion undergoes strong modification in such a structure leading to emergence of low-energy quasi-optical branches. Strong phonon spectrum modification is expected to affect carrier relaxation and transport properties.