Abstract The effect of anisotropic non-Kolmogorov turbulence on the evolution behavior of average intensity and coherent vortices for Gaussian Schell-model (GSM) vortex beams is investigated. Based on the extended Huygens–Fresnel principle and power spectrum of the anisotropic non-Kolmogorov turbulence, the analytical expressions for the cross-spectral density and average intensity of GSM vortex beams propagating through anisotropic non-Kolmogorov turbulence are obtained. The evolution behavior of intensity and coherent vortices for GSM vortex beams in anisotropic non-Kolmogorov turbulence has been discussed in detail by numerical simulation. The results shown that the evolution behavior of coherent vortices and intensity profile depends on the effective anisotropic factor, generalized exponent factor and structure constant of anisotropic non-Kolmogorov turbulence, as well as the beam parameters, such as beam waist, wave length and correlation length.