The thermal effects, produced by the high energy laser in a beam control system, are numerically analyzed in this paper. The effects on the laser density and beam facula quality at far field are studied in particular. The propagation of laser is described by the paraxial wave equations, solved by the phase screen technique and the FFT method. The thermal turbulence motion and the air density variation are governed by the complete Navier Stokes equations, so that the variety factors could be in consideration. The Navier Stokes equations are solved by using the LU SGS factorization technique. The numerical results show that, with the additional initial thermal phase at the emitter exit, the energy density and the quality of the laser beam at far field would be prominently degraded for the typical situations.