Climate change and human activities are profoundly reshaping species distributions, yet their combined impacts on plants with dual ecological-economic roles remain poorly understood. This study investigates Xanthium strumarium, a medicinal-invasive plant, across China using an integrated framework of species distribution modeling (Biomod2), niche dynamics (Ecospat), and rhizosphere microbiome analysis (Tax4Fun). Results reveal that human footprint (66.6% contribution), elevation, and slope dominate its distribution, with suitable habitats projected to expand by 8.9–28.6% under future scenarios (SSP1-2.6 to SSP5-8.5), particularly in Yunnan, Guangdong, and Inner Mongolia. Despite high niche conservatism (Schoener’s D = 0.8986–0.9338), ecological adaptability slightly declines under high emissions. Rhizosphere microbial communities, dominated by Proteobacteria and enriched in nitrogen-cycling taxa (Nitrospira, Verrucomicrobia), enhance adaptability through metabolic and environmental response functions, enabling colonization of disturbed soils. These findings highlight the synergistic roles of climate-driven habitat shifts and microbiome-mediated resilience in shaping X. strumarium’s invasion success. The study provides critical insights for managing its dual roles, advocating for strategies that address both anthropogenic drivers and microbial ecology in biodiversity conservation under global change.