With the development of MEMS, micropower has gradually become one of the essential problems in MEMS applications. The structure of the selective emitter radioisotope microbattery is investigated in detail. The working principle of a radioisotope microbattery is discussed at first. Then the design of the radioisotope microbattery is proposed around the aspects of shape structure and doping mode. Next, a prototype of the radioisotope microbattery in three different shape structures with two doping modes is fabricated. Finally, the prototype of the radioisotope microbattery is tested at Beijing Atom HighTech Incorporated. After comparing the selective emitter radioisotope (SER) microbattery and back surface field (BSF) microbattery, the results indicate the characteristic of the SER microbattery has better performance with the type of inverted pyramid array and V channel array.