Dislocations are important for their effects on the chemical, electrical, magnetic, and transport properties of oxide materials, especially for electrochemical devices such as solid fuel cells and resistive memories, but these effects are still under-studied at the atomic level. We have developed a quantum mechanical/molecular mechanical (QM/MM)-based multiscale simulation program to reveal the diffusion properties of protons on 〈100〉 edge dislocations in BaZrO3 perovskite oxide. We find that the large free space and the presence of hydrogen bonds in the dislocation core structure lead to significant trapping of protons. The diffusion properties of protons in dislocation cores were investigated, and no evidence of pipeline diffusion was found from the calculated migration energy barriers, which not only did not accelerate ion diffusion but rather decreases the conductivity of ions. The proton diffusion properties of Y-doped BaZrO3 (BZY), with a dislocation core structure (BZY-D) and with a grain boundary structure (BZY-GB) were also compared. In all three structures, local lattice deformation occupies an essential part in the proton transfer and rotation processes. The change in bond order is calculated and it is found that the interaction with oxygen and Zr ions during proton transfer and rotation controls the energy barrier for local lattice deformation of the O-B-O motion, which affects the proton diffusion in the structure. Our study provides insight into proton diffusion in dislocations in terms of mechanical behavior, elucidates the origin of the energy barrier associated with proton diffusion in dislocations, and provides guidance for the preparation and application of proton conductors.