In copper electrodeposition under a magnetic field parallel to an electrode surface, at the initial stage, 3D nucleation is suppressed, yielding a flat surface (the first micro-MHD effect). However, after long-term deposition with proton adsorption, characteristic secondary nodules emerge from 2D nucleation, which is called the second micro-MHD effect. From the instability analysis of nonequilibrium fluctuations, at the initial stage, the 2D nuclei are selforganized at a negative overpotential of the double layer, whereas for the secondary nodule formation, a positive overpotential of the double layer is required. Therefore, it is concluded that the adsorption of proton changes the polarity of the double-layer overpotential from negative to positive, so that the secondary nodules is self-organized.