While the water storage capacities of the upper 700 km depths of the mantle have been constrained by high-pressure experiments and diamond inclusion studies, the storage capacity of the lower mantle remains controversial. A recent high-pressure experimental study on CaSiO3 perovskite, which is the third most abundant mineral in the lower mantle, reported possible storage of H2O up to a few weight percent. However, the substitution mechanism for H in this phase remains unknown. We have conducted a series of density functional theory calculations under static-lattice conditions and high pressures to elucidate hydration mechanisms at the atomic scale. All of the possible dodecahedral (Ca2+ → 2H+) and octahedral (Si4+ → 4H+) substitution configurations for a tetragonal perovskite lattice have very small energy differences, suggesting the coexistence of multiples of H configurations in CaSiO3 perovskite at mantle pressures and temperatures. The dodecahedral substitutions decrease the bulk modulus, resulting in a smaller unit-cell volume of hydrous CaSiO3 perovskite under pressure, consistent with the experimental observations. Although the octahedral substitutions also decrease the bulk modulus, they increase the unit-cell volume at 1 bar. The H atoms substituted in the dodecahedral sites develop much less hydrogen bonding with O atoms, leading to a large distortion in the neighboring SiO6 octahedra. Such distortion may be responsible for the non-cubic peak splittings observed in experiments on hydrous CaSiO3 perovskite. Our calculated infrared spectra suggest that the observed broad OH modes in CaSiO3 perovskite can result from the existence of multiples of H configurations in the phase. Combined with the recent experimental results, our study suggests that CaSiO3 can be an important mineral phase to consider for the H2O storage in the lower mantle.