Inspired by the recent experimental synthesis of boron-graphdiyne [Wang et al., Angew. Chem. Int. Ed. 57(15), 3968–3973 (2018)], we have carried out systematic density functional studies on the adsorption and diffusion of alkali metal ions (Li, Na, and K) on boron-graphdiyne monolayer and bilayers, where multiple adsorption sites with strong adsorption energies are identified for all the studied alkali metal ions. Bader charge analysis indicates that significant charge transfer occurs upon absorption, leading to ionic bonding with the substrate and exhibiting a high storage capacity of 1294, 1617, and 1617 mAh g−1 for Li, Na, and K, respectively. Moreover, the migration energy barriers are found in the range of 0.36–0.47 eV for Li, 0.28–0.39 eV for Na, and 0.12–0.32 eV for K. These findings suggest that boron-graphdiyne based materials are promising for ion battery applications.