In order to evaluate the energy conversion performance of micro-thermophotovoltaic system (MTPV) effectively, a novel calculation method combining Fluent with MAT1AB program is proposed, which has considered the non uniformity of temperature distribution of radiant surface, the angular coefficient between the emitter and the PV cell and its cooling efficiency. In this paper, numerical study on hydrogen/air premixed combustion in micro combustors integrated with MTPV system to produce electricity has been adopted. Results show that the overall efficiency of heat recirculation combstor is almost twice as large as obtained in straight channel combustor. Furthermore, dimensionless baffle length, a key parameter in designing micro-combustor with heat recirculation, has been investigated. It is concluded that the subsystem efficiencies of MTPV system are increasing first and then descending with an increase in dimensionless baffle length. However, as the dimensionless baffle length reaches a certain point, the working performance of subsystems changes little. Meanwhile, it is demonstrated that increasing the dimensionless channel gap reasonably will improve the combustion process. Finally, the energy conversion performances as a function of hydrogen volume flow rate are calculated and compared. Results indicate that choosing a proper inlet velocity is of great pivotal to gain a better energy conversion performance of MTPV system. Of all the investigated cases, the maximum power generated with the MTPV is 1.4014 W and the overall efficiency is 0.7092%.