Two-dimensional (2D) metal oxide nanostructure arrays have demonstrated great potential in high performance supercapacitors. The thickness of the 2D nanostructure, the building block of the arrays, has significant influence on pseudocapacitive properties of the arrays, thus their thickness optimization strategy is of great importance to the development of these 2D metal oxide nanostructure arrays, which is eagerly expected but rarely reported. Herein, an integrate hybrid electrode is designed and fabricated via the in-situ synthesis of Co3O4 nanoflake arrays on the nickel@graphene foam via a facile hydrothermal method. Furthermore, the layer number of graphene is adjusted from bilayer to multilayer to investigate the effects of graphene layers on the growth of Co3O4 nanoflake arrays. It is found that the thickness of Co3O4 nanoflakes can be tuned from 70 nm to 13 nm with the increase of the layer number of the graphene sheets due to the different surface diffusion coefficient of Co3O4 nanoparticles. The results of electrochemical measurements demonstrate that the hybrid electrode with the thinner nanoflakes presents higher specific capacitance because of the full utilization of the electroactive Co3O4. Particularly, the Co3O4/graphene/Ni hybrid electrode with 13 nm-thick nanoflake delivers a high specific capacitance of 1.75 F cm−2 at 1 mA cm−2 Additionally, a capacitance increase of 12.2% of the initial capacitance is observed after 5000 cycles at a current density of 10 mA cm−2. Our strategy brings new perspectives on optimizing 2D nanostructure arrays for various structure-sensitive applications.