To clarify the mechanism underlying the effects of invasive plant, Flaveria bidentis, on the community and physiological growth of indigenous plants, a common garden experiment was conducted. To monitor the dynamic growth of plant communities in invaded and non-invaded soils, we further determined the growth and physiological variables of four indigenous plants-Setaria viridis, Bidens maximowicziana, Chenopodium glaucum, and Kochia scoparia. The results showed that the plant community diversity index of F. bidentis-invaded soil was less than that of non-invaded soil, but this difference gradually decreased with time. Flaveria bidentis had significant effect on the growth index of native plants (P < 0.05), but this effect was species-specific. The net photosynthetic rate, stomatal conductance, and transpiration rate of the four native species grown in native soil were significantly higher than those of plants grown in the invaded soil (P < 0.05), signifying the suppression effect of F. bidentis on native vegetation. However, the specific leaf area(SLA), specific root length(SRL), and specific root area(SRA) of the four native species grown in invaded soil were significantly higher than those of plants grown in native soil (P < 0.05), indicating species-specific tolerant strategies to competition from the invader. Overall, the invasion of F. bidentis inhibited the photosynthetic efficiency of native plants and reduced the accumulation of biomass, decreasing the biodiversity level of native plant communities, but it showed seasonal differences. The response of different species to the invasion of F. bidentis showed interspecific difference. The study provides a theoretical basis to understand the influence of invasive species on the native community structure with time and to restore invaded habitats.