<p>The doping effect of protonic hydrogen (H⁺) in amorphous In–Ga–Zn–O (a-IGZO) has recently attracted significant research interest. Here, we systematically investigate H⁺ dynamics in a-IGZO and its impact on the macroscopic transport properties of thin-film transistors (TFTs), by combining density functional theory with quantum transport simulations. We reveal that H⁺ not only disrupts the local formation of the metal–metal (M–M) bond induced by oxygen (O) vacancies, but also passivates their detrimental effects on carrier transport by forming a metal–H (M–H) bond. Moreover, H⁺ can directly bond with O to form O–H bonds, which exert only a minimal additional impact on carrier transport. Our results suggest that, under positive bias stress conditions, H⁺ may suppress the reformation of M–M bonds, which is consistent with suppression of the reversible defect-evolution pathway observed in the simulations. Under H-poor conditions, the formation energy of the M–H bond is −&#xa0;0.39&#xa0;eV, within 0.21&#xa0;eV of most O–H bond formation energies, while transformations between M–H and O–H bonds are hindered by energy barriers exceeding 1&#xa0;eV. Furthermore, by employing a graph neural network to construct a tight-binding model of the defective a-IGZO channel, our quantum transport simulations support the beneficial role of H doping, showing that it enhances device performance through the passivation of M–M bonds. Additionally, in systems without pre-existing M–M bond defects or those containing O–O bond defects, H doping exhibits only a limited impact on device performance. This study provides new insights for passivating defects and enhancing the transport properties and stability of a-IGZO.</p>