Background and aims <p>Flooding-driven gravel encroachment is common in arid alluvial fans. However, the effect of gravel encroachment on the plant community structure remains unclear.</p> Methods <p>We characterized the relationship between flooding-driven gravel encroachment and plant community structure in an arid alluvial fan in China. Meanwhile, a simulation experiment was conducted to evaluate the soil temperature, water retention, and water-holding capacity of soils mixed with 0%, 20%, 40%, 60, and 80% gravel.</p> Results <p>The percentages of gravel in the soils of five representative plant communities, <i>Stipa breviflora</i>, <i>Stipa tianschanica</i>, <i>Convolvulus tragacanthoides</i>, <i>Ephedra rhytidosperma</i>, and <i>Salsola laricifolia</i> was 34.71%, 38.68%, 61.71%, 64.30%, and 65.95%, respectively. A further simulation experiment revealed that soil temperature increased, yet soil water retention and water-holding capacity decreased as the gravel percentage increased. The density, coverage, biomass, and importance value of perennial herbs decreased, whereas those of shrubs increased with increasing gravel percentage in the soils. Thus, gravel encroachment led to an alteration from perennial herb-dominant communities to shrub-dominant communities owing to soil moisture deterioration. Although this study also found that shrubs create a beneficial living environment for herbs under their canopy, the niche overlap between perennial herbs and shrubs in shrub-dominant communities was significantly promoted. Consequently, gravel encroachment resulted in lower community stability in shrub-dominant communities.</p> Conclusion <p>Flooding-driven gravel encroachment has reshaped the plant community structure and reduced the community stability of this arid alluvial fan. Moreover, the shrub-dominant communities may difficult recover to perennial herb-dominant communities in arid alluvial fans with flooding become more intense.</p>