[Aim] The abundance of the beneficial bacterium—Bacillus cereus in roots (in-root, rhizosphere soil) of Ageratina adenophora (invasive and native populations) and its response to plant allelochemicals were determined. The findings of this study aimed to provide a scientific basis for revealing the changes and mechanisms of the interactions between the invasive A. adenophora and beneficial bacteria. [Method] Three native and three invasive populations of A. adenophora plants from Mexico (M, invasive) and Yunnan (C, native) were used in this study. The common garden method and molecular quantification technology were used to detect the abundance of B. cereus in the roots of native and invasive plants. The effects of allelochemicals on the abundance of B. cereus in soil were investigated using leaf leachates and root exudates of A. adenophora plants from all six populations. [Result] The abundance of B. cereus in the roots of the invasive populations of A. adenophora were higher than those of the native populations, and the abundance from the invasive population C2 was 1172% higher than that of the native population M1. In the rhizosphere soil, the abundance of B. cereus in the three invasive populations was higher than that in the two native populations (M1 and M3), two years from planting. Treatment with leaf leachates and root exudates from different populations of A. adenophora increased the abundance of B. cereus in soil. [Conclusion] The abundance of B. cereus in the roots and rhizosphere soil increased when invasive A. adenophora is grown, which could enhance the positive feedback effects of beneficial bacteria on invasive plants.