The flow structures and heat transfer characteristics of rectangle channel with the new type of vortex generators are obtained using large eddy simulation (LES) and by the application of the hydromechanics software FLUENT6.3. The bevel-cut half-elliptical column vortex generators, which is one model of the passive heat transfer enhancement, are laid on the three-dimensional rectangle channel. The instantaneous characteristic and the variational law of various parameters, such as the velocity, the temperature, the pressure and the vorticity magnitude, is analyzed to find out the temperature stripe structure that is similar with the velocity stripe in the temperature field. A turbulent boundary layer interacting with the disturbance of the vortex generators, is investigated using a “coherent structure” type of approach. The coherent structure and the streak structure of turbulent boundary layer flow are showed and the characteristic of vortex induced by vortex generator and its influence on turbulent coherent structure are analyzed. The control of the coherent structure induced by vortex generator plays more important role in heat transfer enhancement and drag reduction. And this fow configuration is of interest in terms of both heat transfer and skin friction control. The result of simulation indicates that the turbulence coherent structure directly affects the temperature gradient at the wall and the heat transfer enhancement mechanism of vortex generator is explained. Then we can seek suitable form of vortex generator and structure parameters, in order to achieve enhanced heat transfer and flow of drag reduction.