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Modern lean burn combustors are developed to meet environmental requirements of low NOx emissions. Comparing with the rich quench lean combustor, lean burn combustor can produce aggressive swirl fields, higher turbulence intensities and different hot streak patterns at the combustor and turbine interface. The flow structures and heat transfer characteristics of high pressure turbine, especially the nozzle guide vanes (NGVs), are significantly affected by the flow patterns from the upstream combustor. In this paper, unsteady integrated calculations are performed for the full geometry contained two NGVs and a non-reacting swirl combustor. The results of three cases of the full geometry, including positive swirler aligned with passage (Case PSW1), positive swirler aligned with leading edge (Case PSW2) and negative swirler aligned with passage (Case NSW), are compared with a baseline case of only NGV simulations with uniform condition (Case UNF). The results indicate that the core of the swirl migrates near the right NGV pressure side in Case PSW1, and near the left NGV suction side in Cases PSW2 and NSW. Higher intensity of the horse shoe vortices and passage vortices is generated in the three non-uniform cases. Hot streak is closer to the hub in Case NSW than Cases PSW1 and PSW2 at NGV exit. Adiabatic wall temperature distributions are influenced by the hot streak and cold fluid migrations. Nusselt number distributions are influenced by the boundary layer accumulation on the NGV surfaces, and by the secondary flow variations on the endwalls. The flow structure and Nusselt number show the similar distribution patterns in Cases PSW1 and PSW2, especially near the endwalls. While, the Nusselt number and the adiabatic wall temperature are obviously changed by the swirl orientation.