Rationally designing an efficient and stable multifunctional electrocatalyst to replace the noble metal catalysts is extremely demanding but challenging. Herein, we develop a facile method to synthesis the defective nitrogen-doped graphene encapsulated metal nanoparticles by pyrolysis of graphene-supermolecule complexes. The obtained catalyst exhibits superior activities toward ORR (E1/2 = 0.864 V), OER (η =383 [email protected] mA/cm2) and HER (η = 193 [email protected] mA/cm2) in 0.1 M KOH solution. Equipping the materials into a rechargeable zinc-air battery produces a peak power density of 205 mW/cm2 and a cycle life of 667 h. It is found that formative M–Nx and defective N-doped graphene are the main origins of ORR activity while OER and HER activities are attributed to the defect-rich N-doped C and Co core. This finding provides insights to design electrocatalyst with both multifunctional catalytic activities and high stability.