The diffusion mechanism of hydrogen atom in α-quartz was investigated by using Ab Initio Molecular Dynamics(AIMD) under different temperatures (300 K,700 K,1 000 K,1 200 K) and the activation energy(0.078 eV) and pre-factor D0(7.72×10-4cm2/s) were calculated by Einstein relation. The study demonstrates that there are two paths of diffusion of hydrogen atom in α-quartz. Under low temperatures, the hydrogen atom mainly moves in a network of cavities connected by silicon and oxygen atoms until it jumps from a ring to another cavity. In addition,the diffusion of hydrogen atom at 1 500 K has also been studied. The hydrogen jumps among the three oxygen atoms, resulting in three types of defect structures during the diffusion, which can be converted to each other. To clarify the diffusion mechanism of hydrogen atoms in quartz has important applications in reliability analysis of microelectronic devices.