With the rapid development of wind power, there are increasing concerns about the negative ecological effects of its construction and operation. However, previous studies have mainly focused on the effects of wind farms on flying fauna (i.e., birds and bats) or climate change separately from communities or ecosystems, and little attention has been paid to vegetation during wind farm operation. Furthermore, few studies have referred to vulnerable ecosystems with low biomass and biodiversity. In this research, a field study was conducted to investigate the effects of wind farms on the individual traits, community structures and ecosystem functions of Gobi Desert ecosystems. The effects were measured by comparing interfering areas (IAs, located between 40 m and 90 m in the downstream direction of the wind turbine) with non-interfering areas (NIAs, located over 200 m from the wind turbine matrixes). The results showed that (1) plant individuals in IAs were less stressed and in better physiological states than those in NIAs; (2) for community structures, IA plants tended to be shorter and denser and had a higher coverage condition than that of NIA plants; and (3) ecosystem functions in IAs were significantly improved due to the existence of shrubs and higher biomass. Meanwhile, significant correlations were identified between the wind wake caused by the large spinning blades and the community structures. Constructing wind turbines in the Gobi Desert is a win-win strategy that both contributes to the growth of desert vegetation with a favourable microclimate and sufficiently utilizes wind power to produce clean energy.