The hierarchy of the coupling strengths in a physical system often engenders an effective model at low energies where the decoupled high-energy modes are integrated out. Here, using neutron scattering, we show that the spin excitations in the breathing pyrochlore lattice compound CuInCr$_4$S$_8$ are hierarchical and can be approximated by an effective model of correlated tetrahedra at low energies. At higher energies, intra-tetrahedron excitations together with strong magnon-phonon couplings are observed, which suggests the possible role of the lattice degree of freedom in stabilizing the spin tetrahedra. Our work illustrates the spin dynamics in CuInCr$_4$S$_8$ and demonstrates a general effective-cluster approach to understand the dynamics on the breathing-type lattices.