The application of 3D printing technology in the field of energy storage is of great practical significance but still remains challenging. Recently, 3D-printed graphene-based architecture has been found to be a promising material for electrochemical energy storage devices. In this study, graphene-based conductive filaments were printed through direct ink writing method (DIW), and then dense poly-pyrrole film (PPy) was formed on the surface of the 3D frame by simple electrodeposition. And followed by post treatment three-dimensional heterogeneous graphene-based electrodes wrapped by nanocarbon cloth (3DCGs) were readily prepared. 3D-printed open porous structure provides effective aligned channels for ion transport as well as large ion accessible area for electrochemical reaction. PPy layer helps to maintain the structural integrity and obtain high capacitance retention rate. A series of 3DCGs with controllable channels were prepared by adjusting the number printing layers, infilled spacing and nozzle size. Thus, we gained an insight into the influence of structural engineering of electrode materials on electrochemical performance. The 5-layer 3DCG with filament spacing of 300 µm and filament diameter of 400 µm achieved an areal capacitance of 2265.19 mF/cm2 at a scan rate of 5 mV/s, which was significantly higher than that of non-3DCG (400.15 mF/cm2). Briefly, this study reports the integration of DIW 3D-printing and electrodeposition techniques allowing a facile way of fabricating customized 3D-electrodes with large areal capacitance.