Using non-equilibrium Green's functions' technology combined with small polaron transformation, we theoretically study the inelastic spin Seebeck effects in a controllable Aharonov–Bohm interferometer based on a degenerate molecular quantum dot level. The numerical results show that when the direct coupling between electrodes is switched on, the spin-dependent thermoelectric efficiency will be suppressed, but the magnetic flux can modulate the thermoelectric line-shapes regularly and the pure spin current generation can be achieved by the temperature gradient. When the direct coupling between electrodes is closed, the spin-dependent thermoelectric efficiency will be raised greatly and the heating resulting from the electron–phonon coupling can improve it effectively.