The Eupatorium adenophorum have widespread invaded the karst ecosystem of southwest China and threatened the regional native community stability. Arbuscular mycorrhizae (AM) plays an important role in promoting growth for host plants via root external mycelia. However, whether AM regulates plant root traits underlying competition between invasive and native species via mycorrhizal networks in karst habitats, remains unclear. An experiment was conducted in a microcosm composed of two planting compartments flanking a competition compartment. The invasive E. adenophorum and native Artemisia annua were each placed in one of the two planting compartments with or without Glomus etunicatum fungus. The nutrient access treatments included the competitive utilization (Cu), single utilization (Su) and non-utilization (Nu) by using different nylon meshes allowed or prevented mycelium passing to acquire nutrients from the competition compartment. Root traits and nutrients of the two species were analyzed. The results showed that AM fungi had differential effects on root traits and nutrients of E. adenophorum and A. annua seedlings, which increased dry weight, length, surface area, volume, tips and branching points in roots, specific root length and volume, root nitrogen (N) and phosphorus (P) contents under Cu, Su and Nu treatments. AM fungus was also associated with decreases in the average diameter for both species. Under the Cu treatment, E. adenophorum had significantly greater length, surface area, volume, tips and branching points of roots, specific root traits, and root N and P than A. annua. AM fungi changed root phenotypes and nutrient uptake for both invasive and native plant species via interconnected mycorrhizal networks. Overall, our results suggest that through mycorrhizal networks, the invasive plant experiences greater benefits than the native plant in the nutrient competition, which fosters root morphological developments in karst soil.