A major concern in the Computational Fluid Dynamics (CFD)-based throughflow calculation is the treatment of the incidence and deviation. This paper investigates the effects of the incidence and deviation on the CFD-based throughflow analysis by a time-marching throughflow model. The model is realized by solving complete Navier-Stokes equations with a single grid in the g-wise direction. The inviscid blade force is determined by calculating a pressure difference between the pressure and suction surfaces. The losses are introduced by imposing a blade surface skin friction factor converted from the pressure loss coefficient. And the flow discontinuity problem at the leading and trailing edges is resolved by modifying the mean blade surface to accommodate the incidence and deviation. The sensitivity of the throughflow results to the modification strategy of the mean blade surface is studied through response surface method. And the Kriging-assisted genetic algorithm (GA) is applied to determine the optimal distributions of incidence and deviation in the streamwise direction for NASA Rotor 37. Finally, four examples are provided to validate the throughflow model and to demonstrate the effects of incidence and deviation on CFD-based throughflow analysis at off-design conditions.