Helium diffusion in carbonate minerals is important for studying the physical and chemical properties and dynamic processes of Earth’s degassing. This paper discussed helium incorporation and diffusion mechanism in crystals of calcite and aragonite based on density functional theory calculations. The diffusion pathways, activation energies (Ea), and frequency factors (v) of helium under the surface and mantle condition were calculated. Calculations show an apperant anisotropy of helium diffusion in calcite, with more energetically favorable directions along a(b) axis. The moderate anisotropy of helium diffusion is showed in aragonite, in which the diffusion rate along c axis is slower than that along a axis. Under high pressure conditions, the activation energies of helium diffusion in aragonite increase with pressure. The closure temperature for calcite crystal varies from −54 ℃ to −25 ℃ in the direction , and for aragonite varies from −12 ℃ to 23 ℃ in . Aragonite may be more retentive for helium than calcite under surface condition, which agrees well with previous experimental studies.