Effects of non-axisymmetric endwall profiling on total pressure loss, heat transfer and film cooling effectiveness of a transonic rotor blade were numerically investigated. The numerical methods, including the turbulence model and grid sensitivity, were validated with the existing experimental data. To reduce thermal load on endwall, non-axisymmetric endwall profiling near leading edge and at pressure-side corner area were performed with a range of contour amplitudes. Heat transfer and flow fields near the profiled endwalls were analyzed and also compared to the plain endwall configuration. On the profiled endwall, three kinds of cooling-holes, i.e. cylindrical holes, rounded-rectangular holes and elliptical holes, were arranged, and film cooling effect was investigated at three blowing ratios. Results indicate that, with endwall profiling, the area-averaged Stanton number on endwall is reduced by 7.71% and total pressure loss in cascade is reduced by 11.07%. Among three kinds of cooling holes, arrangement of elliptical hole performs the best film cooling effect on profiled endwall. Compared with plain endwall, non-axisymmetric endwall with elliptical cooling holes improves film cooling coverage by 10.87%, reduces the Stanton number by 8.88% and increases the net heat flux reduction performance by 4% at M = 0.7.