Complex [Fe3O(O2CPh)6(py)3]ClO4·py (1) crystallizes in the hexagonal P63/m space group, and its cation exhibits a crystallographically imposed D3h symmetry due to a C3 axis passing through the oxide of its {Fe3O}7+ core. Single-crystal unit-cell studies carried out with synchrotron radiation confirmed that this symmetry is retained down to 4.5 K; a full crystal structure determination carried out at 90 K resolved the previously reported disorder of the perchlorate anion. Magnetic susceptibility and electron paramagnetic resonance (EPR) data for complex 1 were interpreted with a model considering the retention of the threefold crystallographic symmetry while predicting a lowering of the magnetic symmetry. This model considered the effects of atomic vibrations of the central oxide on the magnetic properties of the complex by incorporating these movements into the spin Hamiltonian through angular overlap considerations of the atomic orbitals; no ad hoc magnetic Jahn-Teller effect was considered. The derived magnetostructural correlations achieved an improvement in the interpretation of the magnetic susceptibility data using the same number of free variables. They also improved the simulations of the EPR data, which exhibit a complicated set of at least five axial resonances; improved simulations were achieved using only two spectral components. Due to the thermal effects on the oxide vibrations, the model predicts a temperature dependence of the magnetic coupling J, which should not be viewed as a constant but as a variable.