Considering of the complex wave number, the second-order intensity moments and the M2-factor of partially coherent beams have been modified. A partially coherent Gaussian Schell-model beam progating in media is taken as typical example to study the change of M2-factor. It can be shown that unlike in free-space, the M2-factor of partially coherent beams in the gain or absorbing media does not only depend on the coherent parameter β. In gain media, the M2-factor increases with the increase of the propagation distance B and the parameter characterizing the media Ki, and with the decrease of the coherent length σ0 and the wave number Kr, whereas in absorbing media, the M2-factor decreases with the increase of the propagation distance B and the parameter characterizing the media Ki, and with the decrease of the coherent length σ0 and the wave number Kr. The result can offer some effective methods of beam quality control.