The protonation-controlled conductance switching of 4,4 '-vinylenedipyridine (44VDP) molecular junctions was experimentally reported by Brooke et al.(Nano Lett 18(2): 1317-1322, 2018), where a change induced by protonation in the bonding at the molecule-metal interface was proposed as the key ingredient. Here, we perform a first-principles study on the spin-dependent transport properties of 44VDP molecular junctions modulated by protonation. The switching mechanism in the experiment is clarified; namely, the weak coupling strength at the molecule-metal interface is triggered by protonation of pyridyl groups in the 44VDP molecule. In particular, the protonation process modifies the organic-ferromagnetic spinterface, which reduces the number of hybrid interface states and causes an inversion of tunneling magnetoresistance from positive to negative values. Furthermore, a protonation-induced excellent spin-filtering effect is realized. This work sheds light on the mechanism of protonation at the organic-ferromagnetic interface and provides a promising way to realize multifunctional devices in organic spintronics.