In this paper, we study the asymptotic behavior for the incompressible anisotropic Navier–Stokes equations with the non-slip boundary condition in a half space of \({\mathbb{R}^3}\) when the vertical viscosity goes to zero. Firstly, by multi-scale analysis, we formally deduce an asymptotic expansion of the solution to the problem with respect to the vertical viscosity, which shows that the boundary layer appears in the tangential velocity field and satisfies a nonlinear parabolic–elliptic coupled system. Also from the expansion, it is observed that away from the boundary the solution of the anisotropic Navier–Stokes equations formally converges to a solution of a degenerate incompressible Navier–Stokes equation. Secondly, we study the well-posedness of the problems for the boundary layer equations and then rigorously justify the asymptotic expansion by using the energy method. We obtain the convergence results of the vanishing vertical viscosity limit, that is, the solution to the incompressible anisotropic Navier–Stokes equations tends to the solution to degenerate incompressible Navier–Stokes equations away from the boundary, while near the boundary, it tends to the boundary layer profile, in both the energy space and the L∞ space.