The coupling between electronic spins and lattice vibrations is fundamental for driving relaxation in magnetic materials. The debate over the nature of spin-phonon coupling dates back to the 40s, but the role of spin-spin, spin-orbit and hyperfine interactions, has never been fully established. Here we present a comprehensive study of the spin dynamics of a crystal of Vanadyl-based molecular qubits by means of first-order perturbation theory and first-principles calculations. We quantitatively determine the role of the Zeeman, hyperfine and electronic spin dipolar interactions in the direct mechanism of spin relaxation. We show that, in a high magnetic field regime, the modulation of the Zeeman Hamiltonian by the intra-molecular components of the acoustic phonons dominates the relaxation mechanism. In low fields, hyperfine coupling takes over, with the role of spin-spin dipolar interaction remaining the less important for the spin relaxation.