Three types of carbon nano-onions (CNOs) including Ni@CNOs, Fe3C@CNOs and Fe0.64Ni0.36@CNOs nanoparticles have been synthesized by catalytic decomposition of methane at 850 °C using nickel, iron and iron-nickel alloy catalysts. Comparative and systematic studies have been carried out on the morphology, structural characteristics and graphitic crystallinity of these CNOs products. Furthermore, the electrochemical hydrogen storage properties of three types of CNOs have been investigated. Measurements show that the Ni@CNOs have the highest discharge capacity of 387.2 mAh/g, corresponding to a hydrogen storage of 1.42%. This comparison study shows the advantages of each catalyst in the growth of CNOs, enabling the controllable synthesis and tuning the properties of CNOs by mediating different metals and their alloy for using in the fuel cell system.