Micro mechanical energy harvester as a kind of micro power source for micro electro mechanical systems (MEMS) has been paid considerable attention. Electret-based vibration energy harvester (E-MVEH) has been a research highlight due to its high sensitivity, simplicity and compatibility to the fabrication process of MEMS. In this manuscript, a novel E-MVEH with multiple-air-gap structure based on bipolar electrets is comparatively investigated. The E-MVEH with single-air-gap structure consists of an electret membrane (EM) with an electrode on one surface and a counter-electrode supported by means of micro-springs. The E-MVEH with double air gaps is made of a bipolar electret membrane put in the middle of two counter-electrodes that are supported by means of micro-springs. It is essentially equivalent to two variable capacitors in series. The E-MVEH with four air gaps consists of two double-air-gaps E-MVEH in parallel connection. When an external vibration causes a relative displacement between the electret membrane (EM) and the counter-electrode, the capacitance varies, leading to re-organization of the charges on the counter-electrode. Thus, an alternating current is generated and the vibration energy is converted into electric energy. This alternating current can be changed into direct current through a full bridge rectifier. The bipolar EM used in this study is a sandwich FEP/THV/FEP perfluoropolymer EM reported previously by our group. It can display persistent and strong electrostatic field with both polarities on the top and bottom surface, respectively. The experimental results of the output characteristic for the proposed E-MVEH show that there exists a resonant frequency in the vibration frequency range of 30−180 Hz, at which the open-circuit voltage and short-circuit current and hence the output power reach their respective maximum. The resonant frequency moves towards the low frequency with increasing vibration intensity, whereas the effect of air-gap number on the resonant frequency is rather small. On the basis of experimental results and theoretical analysis, the maximum output power is positively correlated to the vibration driving force, the surface potential and the area of the electret membrane, and the air-gap number. When the surface potential of the electret membrane is 1200±50 V, the maximum output power is only 0.19 μW for single-air-gap structure and reaches 27.02 μW for the four-air-gap structures under a vibration driving force of 0.5 N and a load resistance of 55 MΩ. For the four-air-gap structures, the maximum output power increases to 59.12 μW when the surface potential of the electret membrane increases to 2150 V. The multi-air-gap energy harvester fabricated with bipolar electret membrane can produce larger variable capacitance; therefore, the output power is significantly enhanced. This novel E-MVEH provides an up-to-date strategy for the design of self-powered sensor systems.