A pair of flexible flags clamped vertically in a heated channel was 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. The flexible flags displayed three distinct movement modes: a flapping mode, a fully deflected mode, and an irregular mode that depended on the relationship between the hydrodynamic force and the restoring force. In the flapping mode, vortices shed from flexible flags merged and increased in magnitude. The merged vortical structures swept out the thermal boundary layer and enhanced thermal mixing between the fluid near the heated wall and the channel core flow. Compared to rigid flags, the flexible flags significantly improved the thermal efficiency. The effects of the bending rigidity, channel height, and Reynolds number on the thermal efficiency were observed, and an optimal parameter set was obtained. The presence of the flexible flags with the optimal parameter set resulted in an increase of up to 185% in the net heat flux and 106% in the thermal efficiency factor, compared to the baseline flow. The correlation between the vorticity and the temperature field was examined in detail using the dynamic mode decomposition (DMD) method. (C) 2016 Elsevier Ltd. All rights reserved.