closo-type complex hydrides contain large cage-type complex polyanions in their crystal structures and thus can exhibit superior ion-conducting properties (e.g., Li and Na). However, the unique structures of complex polyanions have made it challenging to modify crystal structures, making systematic control of ion conductivity difficult. Here, we report an atom deficiency approach to enhance lithium-ion conductivity of complex hydrides. We find that lithium and hydrogen could be simultaneously extracted from Li2B12H12 by applying a small external energy, enabling the formation of atom deficiencies. These atom deficiencies lead to an increase in carrier concentration, improving lithium-ion conductivity by 3 orders of magnitude compared to that of a pristine material. An all-solid-state TiS2/Li battery employing atom-deficient Li2B12H12 as a solid electrolyte exhibits superior battery performance during repeated discharge-charge cycles. The current study suggests that the atom deficiency can be a useful strategy to develop high ion-conducting complex hydride solid electrolytes.