The interaction between shock waves and boundary layer in isolator causes a very complicated flow, to simulate the turbulent flow field in it, the time-dependent, implicit, finite volume, lower-upper numerical method was used to solve the 3D compressible Reynolds-averaged Navier-Stokes equations. Numerical results are compared with experimental data and used to describe the vortex structures in different isolator shape or different location of an isolator combined shock train structures in it. The numerical results indicate that the vortex structures in square cross section and rectangular cross section is very different.