In this investigation, Ca deposited B16 structure as a promising hydrogen storage improver system has been evaluated via density functional theory (DFT) approach. The Ca@B16 and 2Ca@B16 structures were designed and their adsorption capacities for hydrogen molecules were studied. The Ca@B16 system can absorb up to four hydrogen molecules while 2Ca@B16 can adsorb maximum six hydrogen molecules. Due to the fact that hydrogen adsorption depends on the polarization quality of Ca-B bond of the studied surface, the H2 molecules were adsorbed on the Ca atom(s) of the cluster. Our calculations revealed that the hydrogen gravimetric uptake in the 2Ca@B16 is about 4.7 wt.% with average adsorption energy per hydrogen molecule (< Eads >) of − 1.433 to − 2.518 kcal mol−1. As a result, by manipulating the 2Ca@B16 content, the hydrogen storage capacity can be increased and this small cage may be a candidate material for promoting hydrogen storage process.