The application of grooved surface structure is an emerging and effective means in turbulence flow control. However, for a realistic configuration, the global flow field described directly by simple application of massive grids makes it unfeasible to simulate. In this paper, a boundary surrogate model reproducing the effect of microscopic near-wall region is proposed to improve computational efficiency. The surrogate model trained with Lattice Boltzmann Method (LBM) considering the rarefied effect based on real micro/nanoflow field is new among literature, which accurately shows flow characteristics of the micro/nano structure. With this approach, numerical simulations via Reynolds-averaged Navier Stokes equations with modified wall boundary condition are performed in subsonic and transonic flow. The results show that micro/nano grooved surface structure has the effect of delaying transition from laminar to turbulence, thus reducing the skin friction significantly. Analysis of turbulence intensity and turbulence kinetic energy shows that the near-wall flow field of grooved airfoil is more stable compared with that of the smooth airfoil. The reducing rate of maximum turbulent intensity reaches 13.39%. The paper shows a perspective for further application of micro/nano groove structure to turbulence flow control in aircraft design by providing an accurate and efficient simulation method.