This study numerically and experimentally examined the effects of pin fin configuration and channel geometry on the performance of a hexagonal mini-channel heat sink (HMCHS) to cool cylindrical lithium-ion battery cells. Various configurations of HMCHS with circular pin fins are studied, including circular fins centrally positioned within flat channels, circular fins positioned within grooved channels, circular fins situated within hybrid channels transitioning between wavy and straight channels and circular fins placed within hybrid channels that incorporate secondary flow channels between the primary flow channels. This numerical study utilized the finite volume method to investigate the laminar water flow at Reynolds numbers below 800. Findings showed that the HMCHS exhibited superior thermal performance compared with the conventional cylindrical mini-channel heat sink design. Moreover, the incorporation of pin fins into the HMCHS design was more effective in enhancing the Nusselt number than simply increasing the Reynolds number across various configurations. Meanwhile, the hybrid channel design with secondary channels, combined with the addition of pin fins, achieved the optimal overall performance of the HMCHS, resulting in the highest performance index of 1.88.