The flow characteristics and heat transfer performance of a rectangular channel with a small-scale circular cylinder vortex generator are numerically investigated with Large Eddy Simulation (LES). The circular cylinder is located in fully-developed turbulent boundary layer. The ratio of the gap between the circular cylinder and the channel bottom to the diameter of the circular cylinder G/D, varies from 0 to 6.0. The Reynolds number, based on the bulk velocity um and channel half-height H, is 3745. The influence of the circular cylinder wake on the wall boundary layer is probed. In addition, the effects of the presence of the small-scale vortex generator on the flow and heat transfer characteristics are investigated as well. The synthesis efficiency of heat transfer enhancement is characterized by the synthesis performance coefficient, which including Nusselt number and friction coefficient. The result shows that the interaction between the cylinder wake and the wall boundary layer can dramatically alter the flow structure of the turbulent boundary layer. The thermal performance of rectangular channel with small-scale vortex generator is improved prominently.