Heterogeneous heating of the laser beam is one of the most important effects on the beam propagating through the atmosphere. For the intensity distribution of the flat-topped rectangular beam, the rotary laser beam is adopted to weaken the thermal effects induced by the heterogeneous beam intensity distribution. Based on the computational fluid dynamics(CFD) software of Fluent, thermal effects of the beam in the line pipe with axial pipe flow are modeled. The results indicate that the second order astigmatism which is one of the greater components of optical path difference(OPD) induced by the heterogeneous beam intensity distribution is almost vanished because of the rotary laser beam, while the defocus and the spherical aberration which are the other greater components of the OPD are still exist. The effect of rotary laser beam does not affect the time of the thermal effects reaching the steady state. So the rotary beam effect can improve the beam propagating property.