This paper shows the optimization of the structure of the electromagnetic energy harvester consisting of the sputtered NdFeB film on high aspect ratio Si trench and the Au serpentine coil. The magnetic flux density change is caused by distance change between coil and magnet film on the corrugated Si. In order to maximize the harvesting energy, the optimum parameters such as width, depth of Si trench, and coil size are investigated by FEM analysis and theoretical calculation. Assuming the trench depth of 400 μm the vibration amplitude of 400 μm_<p-p> and the frequency of 100 Hz the maximum output power of 12 nW and the maximum electromotive force of 4 mV are obtained by 60 μm and 80 μm, respectively.