[Objective] The influences of flooding on the growth and plant diversity of typical riparian forest communities in the desert was quantitatively analyzed in order to provide a theoretical basis for improving the scientific water replenishment plan and the efficient use of ecological water in arid area.[Methods] Data were obtained from vegetation surveys in the upper and middle reaches of the Tarim River from 2016 to 2018. The impacts of flooding were analyzed using the Pielou index, Shannon-Wiener index, Simpson index and important values.[Results] After flooding for 2 years, 11 new plants were found in the upper and middle reaches of the Tarim River, mainly Populus euphratica, Tamarix chinensis, hygrophilous plant and annual herb. The density of P. euphratica increased by 0.72 plants/m², with a growth rate of 855.9%. The new branch length of T. chinensis increased by 41.8 cm, and the growth rate was 71.58%. The growth of P. euphratica was significantly improved as the occurrence of good quality P. euphratica increased by 0.11 plants/m² with a growth rate of 32%. With the increase of the distance from ecological gate, the density of P. euphratica forest showed a tendency of decrease, and the aging of the forest became more prominent. The species diversity under the forest showed a tendency of decrease with the increase of the flooding distance. Within 300 m from the ecological gate, the seedlings of P. euphratica, T. chinensis and the hygrophilous one year or perennial herb became the dominant species (the important values were 0.243, 0.195 and 0.248, respectively). When the distance was greater than 300 m, the dominant species were gradually replaced by perennial herbs of T. chinensis and drought-tolerant herbs. The annual herb, P. euphratica and T. chinensis disappeared at 450 m away from the ecological gate.[Conclusion] Flooding irrigation enhanced the regeneration ability of plant communities and species diversity in desert riparian forests. In order to maintain the current ecological improvement trend, the flood irrigation project needs to be continued.