Due to the use of heavily doped N type silicon substrate, the nuclear micro-battery based on silicon PN diode suffers from the small minority carrier life-time and small depletion region width, and can not achieve high energy transfer efficiency. A nuclear micro-battery utilizing silicon PIN diode as the energy transfer structure was demonstrated with achieves higher electrical power output. Theoretical model was built to predict the power output performance of this kind of micro-nuclear battery and structure optimization was performed in terms of the stopping range of beta particles, the depletion region width, the minority carrier life-time and the body resistance. Prototypes of PIN energy transfer structure were fabricated and were illuminated by using beta radioisotopes 63Ni,147Pm and alpha radioisotope 241Am as the radiation sources, and proved to be effective to improve the energy transfer performance.