To design molecular spin qubits with enhanced quantum coherence, a control of the coupling between the local vibrations and the spin states is crucial, which could be realized in principle by engineering molecular structures via coordination chemistry. To this end, understanding the underlying structural factors that govern the spin relaxation is a central topic. Here, we report the investigation of the spin dynamics in a series of chemically designed europium(II)-based endohedral metallofullerenes (EMFs). By introducing a unique structural difference, i. e. metal-cage binding site, while keeping other molecular parameters constant between different complexes, these manifest the key role of the three low-energy metal-displacing vibrations in mediating the spin-lattice relaxation times (T1). The temperature dependence of T1 can thus be normalized by the frequencies of these low energy vibrations to show an unprecedentedly universal behavior for EMFs in frozen CS2 solution. Our theoretical analysis indicates that this structural difference determines not only the vibrational rigidity but also spin-vibration coupling in these EMF-based qubit candidates.