Miniaturized and smart energy storage devices are highly demanded due to the enormous development and miniaturization of advanced on-chip electronic systems. Micro-supercapacitors (MSCs) with ultra-high peak power density and long-term stability can fulfill the requirements for practical applications in microsystems. However, further development of efficient manufacturing techniques with high practicability for high-energy in-plane MSCs is highly challenging. Herein, we fabricate three-dimensional (3D) manganese dioxide (MnO₂) nanotube arrays (NTAs) assembled with intersecting nanoflakes for high-energy on-chip interdigital MSCs which can be produced using a novel and cost-effective membrane transfer process. Owing to the large electroactive surface area, excellent structural stability, remarkable wettability and short transport path of ions and electrons of intersecting nanoflake-built MnO₂ NTAs, the fabricated 3D MSC device exhibits high energy density, excellent cycling stability and desirable flexibility. In addition, the output voltage and capacitance of MSCs can be readily controlled by rational interconnection to satisfy the practical use. The proposed strategy for the fabrication of 3D NTA-based MSCs with high energy and desirable flexibility opens up a new avenue for portable and wearable electronic devices.