The bulk carrier excitation influences the phonon dynamics, which can alter and modulate the surface charge density of topological insulators such as bismuth selenide (Bi2Se3). This work investigates the charge carrier and phonon dynamics in Bi2Se3 grown on various substrates. The orientation of the substrate, the size of the crystallites, and the misfit of the lattice affect the carrier and phonon dynamics. Bi2Se3 thin films are grown under the same growth conditions on SiO2, Si(111), and SiN. Bi2Se3 overlayers exhibit substrate‐dependent charge carrier relaxation channels and phonon dynamics. It is evident from Raman spectroscopy and ultrafast transient absorption spectroscopy that the heterointerface interactions of all three samples affect the vibration modes of Bi2Se3 and coherent acoustic phonon oscillations in the NIR range. At 13.6, 41.2, and 34.4 GHz, the vibration modes of SiO2, Si(111), and SiN are equivalent. The propagation depth of phonon waves is shown by measuring the speed of sound in Bi2Se3 overlayers on SiO2, Si(111), and SiN. This study demonstrates that the surface and bulk‐bound charge carriers of a topological insulator determine the frequency and velocity of the generated sound.