Thermal diffusion in a developed thermal boundary layer is considered as an obstacle for improving the forced convective heat transfer rate of a channel flow. In this work, a novel, self-agitating method that takes advantage of vortex-induced vibration (VIV) is introduced to disrupt the thermal boundary layer and thereby enhance the thermal performance. A flexible cylinder is placed at the centerline of a rectangular channel. The vortex shedding due to the cylinder gives rise to a periodic vibration of the cylinder. Consequently, the flow-structure-interaction (FSI) strengthens the disruption of the thermal boundary layer by vortex interaction with the walls, and improves the mixing process. This new concept for enhancing the convective heat transfer rate is demonstrated by a threedimensional modeling study at different Reynolds numbers (84~168). The fluid dynamics and thermal performance are analyzed in terms of vortex dynamics, temperature fields, local and average Nusselt numbers, and pressure loss. The channel with the self-agitated cylinder is verified to significantly increase the convective heat transfer coefficient. When the Reynolds number is 168, the channel with the VIV improves the average Nu by 234.8% and 51.4% as opposed to the clean channel and the channel with a stationary cylinder, respectively.