Bidens pilosa is recognized as one of the major invasive plants in China. Its invasion has been associated with significant losses in agriculture, forestry, husbandry, and biodiversity. Soil ecosystems play an important role in alien plant invasion. Microorganisms within the soil act as intermediaries between plants and soil ecological functions, playing a role in regulating soil enzyme activities and nutrient dynamics. Understanding the interactions between invasive plants, soil microorganisms, and soil ecological processes is vital for managing and mitigating the impacts of invasive species on the environment. In this study, we conducted a systematic analysis focusing on B. pilosa and Setaria viridis, a common native companion plant in the invaded area. To simulate the invasion process of B. pilosa, we constructed homogeneous plots consisting of B. pilosa and S. viridis grown separately as monocultures, as well as in mixtures. The rhizosphere and bulk soils were collected from the alien plant B. pilosa and the native plant S. viridis. In order to focus on the soil ecological functional mechanisms that contribute to the successful invasion of B. pilosa, we analyzed the effects of B. pilosa on the composition of soil microbial communities and soil ecological functions. The results showed that the biomass of B. pilosa increased by 27.51% and that of S. viridis was significantly reduced by 66.56%. The organic matter contents in the bulk and rhizosphere soils of B. pilosa were approximately 1.30 times those in the native plant soils. The TN and NO3– contents in the rhizosphere soil of B. pilosa were 1.30 to 2.71 times those in the native plant soils. The activities of acid phosphatase, alkaline phosphatase, and urease in the rhizosphere soil of B. pilosa were 1.98–2.25 times higher than in the native plant soils. Using high-throughput sequencing of the 16S rRNA gene, we found that B. pilosa altered the composition of the soil microbial community. Specifically, many genera in Actinobacteria and Proteobacteria were enriched in B. pilosa soils. Further correlation analyses verified that these genera had significantly positive relationships with soil nutrients and enzyme activities. Plant biomass, soil pH, and the contents of organic matter, TN, NO3–, TP, AP, TK, and AK were the main factors affecting soil microbial communities. This study showed that the invasion of B. pilosa led to significant alterations in the composition of the soil microbial communities. These changes were closely linked to modifications in plant traits as well as soil physical and chemical properties. Some microbial species related to C, N and P cycling were enriched in the soil invaded by B. pilosa. These findings provide additional support for the hypothesis of soil-microbe feedback in the successful invasion of alien plants. They also offer insights into the ecological mechanism by which soil microbes contribute to the successful invasion of B. pilosa. Overall, our research contributes to a better understanding of the complex interactions between invasive plants, soil microbial communities, and ecosystem dynamics.