Abstract Alternative cooling systems that can be used for thermal management in different technological applications such as in batteries, solar panels, electronic systems and in diverse heat transfer equipments are needed. This study uses a hybrid channel system with rotating circular cylinders to explore the cooling of two heated elastic plates. The numerical analysis of a coupled fluid-structure-thermal system with rotating cylinders is done using the finite element technique with ALE. The study is carried out for different values of the Reynolds number (Re) in the upper channel flow (between 200 and 1000), the non-dimensional rotational speeds of the cylinders (Ω in the range between -1000 and 1000), and the non-dimensional location of the cylinders (between 0.4 and 1) taking into account the cooling of both the rigid and elastic plates. Rigid plates have better cooling performance than elastic ones. The cooling performance increases for both rigid and elastic plates reach up to 26.1% and 31.7% at the maximum upper channel flow Re. For elastic and rigid plates, CCW rotation at maximum speed increases cooling performance by 18.5% and 19%, respectively, but CW rotation increments cooling performance by only 7%. By using optimization, the cooling performance increase with rotatingcylinders at Re=200 is determined to be 73.6% more than that of the case without cylinders. Optimization results in an extra 11.2% increase in cooling performance at Re=1000 when compared to the parametric CFD scenario