Body-centered-cubic $\mathrm{Ca}{\mathrm{H}}_6$ has attracted considerable attention due to its unique hydrogen clathrate structure and high-$T_{\mathrm{c}}$ superconductivity ($T_{\mathrm{c}}=215\mathrm{K}$ at 172 GPa). Although hydrogen vacancy in this hydride has been reported experimentally, its effects on structural and superconducting properties remain unclear. By comparing with the experimental equation of state, our path-integral molecular dynamics simulations reveal that pressure reduction induces hydrogen depletion from interstitial sites of the Ca sublattice, resulting in the formation of a nonstoichiometric $\mathrm{Ca}{\mathrm{H}}_{6-\delta }$ phase $\left(\delta \le 0.45\right)$ below 165 GPa. The increase in hydrogen vacancies induces thermoelastic instability below 125 GPa (at 300 K) through shear-modulus softening, while concurrently suppressing superconductivity via electronic-state modulation, with the $T_{\mathrm{c}}$ decreasing at a rate of $2.3\mathrm{K}/\mathrm{GPa}$. Both results align with experimental observations. Moreover, we predict that hydrogen vacancies facilitate hydrogen diffusion in the superconducting $\mathrm{Ca}{\mathrm{H}}_{6-\delta }$ phase between 145 and 160 GPa, with the diffusivity reaching or exceeding ${10}^{-8}\mathrm{c}{\mathrm{m}}^2/\mathrm{s}$. The findings emphasize the key role of hydrogen vacancy in understanding the high-pressure evolution behavior of high-$T_{\mathrm{c}}$ hydrides.

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• High-pressure studies
• Quantum fluids & solids
• Structural properties
• Superconducting phase transition
• High-temperature superconductors
• Hydrides