The great development of lightweight and portable smart electronic devices has significantly stimulated the interests in exploring and developing miniaturized energy storage systems. High-performance micro-super-capacitors (MSCs) with three-dimensional (3D) nanostructures show a great potential to improve energy storage capability, and these types of MSCs are regarded as ideal stand-alone power sources for smart microelectronics. Here, Cu0.56Co2.44O4@MnO2 core-shell nanoflowers and carbon nanotubes are integrated into a 3D hybrid asymmetric MSC with a fast, convenient, and scalable production fashion. Due to the hierarchical structure of the 3D electrodes and active materials, the hybrid MSC exhibits an improved specific areal capacitance of 665.3 mF cm(-2) at 3.2 mA cm(-2) and an excellent cycling performance of 89.8% retention after 8000 cycles. The MSC also shows an ultrahigh energy density of 182.3 mu W h cm(-2), which is higher than almost all the previously reported energy density values of on-chip interdigital-electrode MSCs. The efficient fabrication methodology of both the materials and the device demonstrated in this work show great potential in developing high-performance 3D MSCs.