Aims <p>Intraspecific competition among invasive plants is very common; however, how phyllosphere and rhizosphere microbes influence intraspecific competition of invasive plant and native plants at different seedling densities remains to be characterized.</p> Methods <p>In this study, we used the invasive plant <i>Ageratina adenophora</i> and two native plants (<i>Senecio scandens</i> and <i>Achyranthes bidentata</i>) to evaluate the effects of positions (phyllosphere, rhizosphere), plant sources (<i>A.adenophora</i>, <i>S. scandens</i>, <i>A. bidentata</i>), seedling densities (1, 2, 4, 6 plants), and microbial sources ("live", "dead").</p> Results <p>With intraspecific competition, both phyllosphere and rhizosphere microbes benefited <i>A. adenophora</i> more than without competition; phyllosphere microbes favored <i>A. adenophora</i>, whereas rhizosphere microbes favored <i>A. bidentata</i>. Without competition, phyllosphere microbes (especially for natives) promoted host growth. For <i>A. adenophora</i>, conspecific microbes were more beneficial than heterospecific microbes under competition (opposite for <i>S. scandens</i>). At 2- and 6-seedling densities, microbes benefited <i>A. adenophora</i> more than they did without intraspecific competition; <i>A. bidentata</i> grew better at 2-seedling density under competition. High-throughput sequencing revealed that the inocula rhizosphere and phyllosphere presented distinct microbial community functional structures across plant species, with pathogenic and growth-correlated ASVs driving host-specific microbial effects on competitive performance.</p> Conclusions <p>Our findings contribute significantly to understanding plant-microbe interactions during intraspecific competition, offering new insights into the coexistence of species and the process of plant invasion.</p>