Numerical study on heat transfer characteristics and the turbulent structure is carried out in a three-dimensional turbulent boundary layer with longitudinal vortices. Longitudinal vortices are capable of strongly perturbing of the turbulent and thermal boundary layer, which cause the anisotropy of turbulent intensities and augmentation of heat transfer. This paper uses the Reynolds-stress model(RSM) to capture anisotropy of turbulent structure effectively and the eddy-diffusivitv model for predicting thermal boundary layer. It can be concluded for turbulent flow that the RSM can produce the more accurate predictions for capturing the anisotropy than the standard k-ε model. Also, results of heat transfer show that the disturbing of boundary layer cause the highest level of Stanton number in the region which the flows are directed toward the wall, but the vortices core is a region of relatively lower mixing. By and large, results of the RSM are in better agreement with experimental data than those of standard k-ε model.