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As one of the most important micro energy storage devices (MESDs), graphene-based micro-supercapacitors (G-MSCs) possess the advantages of excellent flexibility, long cycle life, affordability and high reliability. In most cases, constructing three-dimensional (3D) graphene networks is widely utilized to promote the permeation of electrolyte and enhance the utilization of active materials. In this work, conventional freeze-drying process is utilized in the fabrication of G-MSCs to constitute 3D interconnected networks micro-electrodes, and further by regulating the composition of inks, carbon spheres (CSs) at different mass loadings are introduced into the graphene scaffolds to further increase the active sites of the micro-electrodes. The fabricated all carbon-based MSC with the optimal mass loading of CSs (0.406 mg cm−2) exhibits a high specific areal capacitance of 17.01 mF cm−2 at the scan rate of 10 mV s−1 and a capacitance retention of 93.14% after 10000 cycles at the scan rate of 500 mV s−1. The proposed microfabrication process is facile and fully compatible with modern microtechnologies and will be highly suitable for large-scale production and integration. Keywords: Three-dimensional, Injecting, Freeze-drying, Mass loading, Supercapacitor