Mercury has a large loss cone difference in its two hemispheres due to the northward shifted magnetic dipole. The precipitation difference of energetic electrons in both hemispheres is poorly understood. We show that the northern precipitation is 2.5‐times higher than for a symmetric loss cone due to the effects of the enhanced whistler instability at the southern hemisphere with the larger loss cone. Simulations including nonlinear pitch angle scattering by the whistler‐mode waves show rapid (tens of milliseconds) electron flux modulation related to the wave subpacket structures by repeated interactions within a discrete wave element. The difference in the nonlinear whistler instability in the two hemispheres should enhance the electron precipitation, which, along with the direct impact effects of solar wind, contributes to Mercury's surface–magnetosphere coupling. Electrons hitting the planet's surface may be a possible factor in the formation of water through the formation of hydroxyl groups.