The rapid development of sensor networks for smart industry requires comparable tiny power sources that can deliver high energetic performance and be mass-produced via the existed semi-conductor process. In this paper, novel 3D in-chip micro-supercapacitors (MSCs) based on hierarchical electrodes were developed through silicon-based microfabrication techniques by depositing graphene nanowall (GNW)/ruthenium oxides (RuOx) core-shell hybrids on the silicon scaffolds that are generated from deep reactive ion etching (DRIE). Conformal coating of RuOx on individual graphene nanoflakes was realized via reactive sputtering technique to benefit capacitance enhancement, while the orderly aligned GNW facilitated fast ions and electrons transfer. By harnessing both the merits of huge active surface area of the 3D hierarchical electrode architectures and the excellent electrochemical behaviors of the GNW/RuOx hybrids, the assembled MSCs exhibited areal energy, power densities of 15.1 μWh cm−2 and 2.49 mW cm−2, respectively. In parallel with our novel in-chip strategy by leveraging the bulk volume of Si substrate to create sidewall for effective area enhancement at footprint, the embedment of electrode nanostructures inside the substrate may also give a new concept of MSCs design towards protecting the fragile electrode materials and making the subsequent device encapsulation with ease.