We derive analytical formulas for average intensity of a partially coherent elliptical vortex (PCEV) beam propagating in a turbulent atmosphere along an uplink path and a downlink path with the help of the extended Huygens–Fresnel principle. Our outcomes reveal that the normalized initial profile with the elliptical annular dark pattern splits and rotates counterclockwise around the major axis of elliptical hollow pattern with increasing the propagation distance in free space and atmospheric turbulence. We also find that the splitting light spots heal into a Gaussian-like spot due to the turbulence effect, smaller ellipticity, larger topological charge, slower healing process. It can be also found that PCEV beam propagates along a downlink path is less affected by atmospheric turbulence in comparison with uplink path. In order to confirm our numerical results, we combine the complex screen method and multi-phase screen method to simulate the propagation of the PCEV beam in atmospheric turbulence. It is indicated that the simulation results are in good agreement with theoretical results. Our findings may be of great significance for the development of the free-space optical communications.