In this paper, electret based vibration energy harvesters are designed and fabricated with perforated electrode based on MEMS technology. Through-holes are distributed on the fixed electrode in the device to optimize the energy harvesting process. The effect of the holes on the output power of the device are analyzed and discussed both in the finite element method (FEM) simulation and the experiments. It can be noticed that the through-holes can effectively lower the squeeze-film air damping force on the moveable proof mass at the atmosphere. Therefore, the energy loss due to the air damping could be reduced, and the output power of the device increases. The effects of the hole diameter and numbers on the output power of our device are also investigated in detail. By optimizing the configuration of the holes, the perforated device with the hole diameter of 400μ m and depth of 100μ m exhibits the highest power output at the low acceleration of 1.84 m/s2, which proves promising application for self-powered electronics in the future.