The micro combustor is the energy source of micro-thermophotovoltaic systems; thus, optimizing its design is one of the key parameters that lead to an increase in output energy. Therefore, to enhance the system’s overall efficiency, this numerical work introduces a new design configuration for parallel-flow (PF) and counter-flow (CF) hydrogen-fueled micro cylindrical combustors integrated into a micro planar combustor. To overcome the short residence time in micro combustor applications causing high heat dissipation, the micro cylindrical combustors house heat-recirculating channels to allow more heat to transfer to the external walls. In pursuit of this target, simulations are carried out to analyze the thermodynamic and system efficiency parameters. In addition, different initial operating conditions are varied to optimize the system, including inlet velocity and equivalence ratio. The results reveal that the PF and CF structures result in significantly higher wall temperatures and more uniform wall temperature variations than the conventional design (CD). Despite the high entropy generations, the exhaust gas temperatures of the PF and CF are 591 K and 580 K lower than the CD, respectively, and both the PF and CF result in 14% increases in radiation efficiency. Increasing the inlet velocity improves the key thermal parameters in the new designs; however, the system efficiency experiences a drastic reduction. The power output density highlights the unity equivalence ratio as optimal. The PF and CF designs yield roughly identical findings, but the CF exhibits more uniform wall temperatures in most cases due to the equal thermal energy from opposite sides.