Two flexible flags clamped in a heated channel were numerically modeled to investigate the dynamics of the flexible flags and their effects on heat transfer enhancement. The penalty immersed boundary method was adopted to analyze the fluid-structure-thermal interaction between the surrounding fluid and the flexible flags. A system comprising the thermally conductive flags in an asymmetric configuration (FAC) with respect to the channel centerline is described for the first time in the present study. The effect of the resulting vortices on heat transfer enhancement was investigated. The FAC generated a reverse Karman vortex street that encouraged a greater degree of thermal mixing in the wake compared to the vortical structures generated by the flags in a symmetric configuration (FSC). The ratio of FAC occupying a cross-section to the channel height decreased, resulting in a decrease in the pressure drop compared to FSC. The FAC significantly improved the thermal efficiency compared to the FSC. The effects of the gap distance between FAC (G/L) and the ratio of the channel height to the flag length (H/L) on the thermal enhancement were characterized to identify the parameters that optimized the thermal efficiency. The relationship between the flapping dynamics and the heat transfer properties was examined in detail. The presence of the FAC with the optimal parameters increased convective heat transfer by 207% and the thermal efficiency factor by 135% compared to the baseline (open channel) flow. The thermal efficiency factor obtained in the present study was compared with that obtained in the previous studies.