Hydrogen generation from hydrolysis of ammonia borane is a secure and promising route for conversion of hydrogen energy. Preparation of efficient and economical catalysts is highly required for the development hydrogen economy. In this study, the Co-based catalysts with multiatomic structure were designed for hydrolysis of ammonia borane reaction. The synergistic effect between Co and M (M = Cu, Ni, Fe) greatly enhanced the catalytic performance of bimetallic catalysts. The TOF value of CoCu-NC-5 towards 8.12 min−1 is 7 times that of the single Co catalyst. Moreover, The CoCu catalysts showed the stronger synergistic effect and highest catalytic activity for hydrogen generation, compared with CoNi and CoFe catalysts. The TOF value of CoCu-NC-5 is 2.3 and 6.0 times that of CoFe-NC-5 and CoNi-NC-5 catalysts, respectively. The active component structure of Cu-CoO/Co interface in CoCu-NC-5 is beneficial for activation and dissociation of water molecule due to the strong electron transfer effect and positive synergy. The activation energy over CoCu-NC-5 is 34.25 kJ mol−1, and the catalyst exhibited good stability. This work provides a feasible method for rational design of efficient catalysts with hierarchical structure for conversion of energy.