Along with the rapid development of miniaturization of mobile devices and wearable integrated electronics system, flexible integrated micro electrical energy storage devices with high-performance, deformability and cycling stability will be the technological trend for a long time in the future. In this work, template plasma etching method and electrochemical deposition method have been combined to fabricate nanoporous gold/manganese oxide interdigitated electrodes that can be easily utilized in flexible micro-supercapacitors(MSCs). These MSCs exhibit relatively high specific capacitance of 18.47 mF cm−2 in 0.5 M Na2SO4 electrolyte and 11.58 mF cm−2 in polyvinyl alcohol (PVA)/LiCl solid state electrolyte. A high energy density of 6.93 × 10−7 Wh cm−2 to 1.03 × 10−6 Wh cm−2 while power density ranging from 4.63 × 10−5 W cm−2 to 3.12 × 10−4 W cm−2. The NPG/MnO2 MSCs excellent long term cycling stability of 80.7% can be seen even after cycling for 5000 times. Moreover, the MSCs devices also demonstrate a sound flexibility and a superior frequency response (1.25 ms). In addition, the effects of various finger width and finger spacing on performance are compared, the critical importance of adjusting interdigitated structure is highlighted. This present research may provide an innovative avenue for the new prospective high-performance flexible micro-supercapacitors.