The flow and heat characteristics of the rectangle channel bottom with a small-scale circular cylinder vortex generator are numerically investigated by large eddy simulation(LES). The vortex generator is located in the turbulence boundary layer. The influence of gap ratio on the flow structure, the Nusselt number and frication coefficient of the channel bottom, and the synthesis performance coefficient is probed. In addition, the numerical channel results by applying LES are in good agreement with the precious results by direct numerical simulation, which verifies the accuracy and reliability of present numerical method. The numerical results indicate that the heat transfer performance at the bottom of channel with small-scale circular cylinder vortex generator is significantly improved and the augmentation of flow resistance is effectively suppressed, compared to that of channel without small-scale circular cylinder vortex generator. The optimal heat transfer performance is obtained when the gap ratio is 2.0, and the Nusselt number is increased by 18.76%. When the gap ratio is 0.5, the drag reduction is the most significant of considered cases and the frication coefficient is reduced by 3.77%