Building of hierarchical core-shell hetero-structures is currently the subject of intensive research in the electrochemical field owing to its potential for making improved electrodes for high-performance micro-supercapacitors. Here we report a novel architecture design of hierarchical MnO2@silicon nanowires (MnO2@SiNWs) hetero-structures directly supported onto silicon wafer coupled with Li-ion doped 1-Methyl-1-propylpyrrolidinium bis(trifluromethylsulfonyl)imide (PMPyrrBTA) ionic liquids as electrolyte for micro-supercapacitors. A unique 3D mesoporous MnO2@SiNWs in Li-ion doped IL electrolyte can be cycled reversibly across a voltage of 2.2 V and exhibits a high areal capacitance of 13 mFcm(-2). The high conductivity of the SiNWs arrays combined with the large surface area of ultrathin MnO2 nanoflakes are responsible for the remarkable performance of these MnO2@SiNWs hetero-structures which exhibit high energy density and excellent cycling stability. This combination of hybrid electrode and hybrid electrolyte opens up a novel avenue to design electrode materials for high-performance micro-supercapacitors.