A supercritical natural laminar airfoil is optimized based on the Bound Optimization BY Quadratic Approximation and Reynolds Averaged Navier–Stokes equations. In the optimization process, the eN method, which is based on linear stability theory, is used for transition prediction. The objective function of the drag coefficient and the airfoil volume as the independent variable is minimized as the optimization target. The effect of grid roughness and the transition prediction of transonic airfoil are studied. Results show that the area of the natural laminar flow area of the optimized airfoil is improved greatly, and the designed lift coefficient and the Mach number have a significant effect on the optimization result.