Heat transfer characteristics of baffled channel flow, where thin baffles are mounted on both channel walls periodically in the direction of the main flow, have been numerically investigated in a laminar range. In baffled channel flow, heat transfer characteristics are significantly affected by large-scale vortices generated due to flow separation at the tips of the baffles. In this investigation, a parametric study has been carried out to identify the optimal configuration of the baffles to achieve the most efficient heat removal from the channel walls. Two key parameters are considered, namely baffle interval (L) and Reynolds number (Re). We elucidate the role of the primary instability, a Hopf bifurcation from steady to a time-periodic flow, in the convective heat transfer in baffled channel flow. We also propose a contour diagram (“map”) of averaged Nusselt number on the channel walls as a function of the two parameters. The results shed light on understanding and controlling heat transfer mechanism in a finned heat exchanger, being quite beneficial to its design.