A capacitor and a manufacturing method thereof are provided. Two electrodes are disposed opposite to each other. Two electrode protection layers are respectively disposed on inner sides of the electrodes and include carbon particles each covered and bonded with a polymer shell. Active carbon layers are disposed on opposite inner sides of the electrode protection layers. The separator is disposed between the active carbon layers. The electrolyte fills between the electrode protection layers. The polymer shells of each electrode protection layer are bonded to the surface of the corresponding electrode by first and second functional groups. The first functional groups include thiol groups. The second functional groups include epoxy groups or carboxylic groups. The electrode protection layers serve as adhesion layers between the active carbon layers and the electrodes, and protect the electrodes from being corroded by the acid electrolyte solution.