The end-to-end axial heterojunction one-dimensional nanoarray combined poly(3,4-ethylenedioxythiophene) (PEDOT) and manganese dioxide (MnO2) have been successfully designed and fabricated. The electrochemical performance was investigated in detail after processing the axial PEDOT/MnO2 heterostructure nanoarray (APMHN) into flexible micro-supercapacitors, namely, PM-MSC. The presence of flexible PEDOT segment effectively improved the conductivity and also provided an important material basis for the preparation of flexible PM-MSC. Further, PEDOT has good contact with both Au substrate and MnO2 segment, ensuring that the charge can quickly shuttle back and forth between the electrode and the current collector. The PM-MSC showed the highest specific capacitance of 209.89 mF.cm(-2) compared with the P-MSC assembled from PEDOT nanoarray and M-MSC assembled from MnO2 nanoarray. The PM-MSC possesses good flexibility, making the capacitance performance of the PM-MSC show almost no deterioration under the 180 degrees bent state. Moreover, several series or parallel PM-MSCs enable a variety of electronic devices to work properly. The APMHN exhibits some new advantages, enabling the integration of physical and chemical properties of the two separate components, while providing a new way of thinking for the design and manufacture of MSC for flexibility.