Abstract Thermophotovoltaics systems involve a thermal-electrical energy conversion process. An energy efficient conversion is desirable for practical applications. In this work, thermal performances and emitter efficiency ( η E ) assessments of two proposed unconventional micro-combustors, i.e. T- and Y-shaped are both experimentally and numerically conducted. Comparison is then made between the proposed combustion systems with the conventional I-shaped micro-combustor with premixed CH4/O2/Ar fueled. The effects of 1) the mass flow rate ( m ˙ ) , 2) the equivalent ratio ( φ ) and 3) the extending depth of the flame holder (H) are numerically investigated using 3D models with structured meshes. The present results show that the thermal performances and the emitter efficiency of both T- and Y-shaped micro-combustors are significantly improved compared to the conventional I-shaped one under same conditions and key construction parameters. Furthermore, it is found that the bifurcation structure (T- and Y-shaped) can reduce the expanding area of the high temperature at the inlet and prevent the wall temperature from dropping too fast at the outlet. When φ is increased to 1.1, the flame position in the T-shaped combustor is found to be shifting away from the outlet of the flame holder, which results in more intensified combustion in the front area. The mean wall temperature shows a great improvement, when an optimal H is chosen. Overall, the Y-shaped combustor presents the best thermal performance with the largest η E of 40.89% and a higher mean wall temperature of 765.1 K, when m ˙ = 4.8 × 10 − 6 k g / s and φ = 0.8 . These findings confirm a significant thermal improvement. This work opens up an energy efficient design of micro-combustors with unconventional structural shapes for thermophotovoltaic applications.