Endophytic bacteria in the roots of a healthy plant not only form a symbiotic relationship with the host plant but also promote plant growth and enhance plant uptake of nutrients, being of importance for maintaining terrestrial ecological balance and improving the comprehensive management of karst rocky desertification. [Objective] To explore the endophytic bacterial communities in the roots of host plants and provide a theoretical basis for deeply understanding the interaction mechanisms between host plants and endophytic bacteria. [Methods] The community structures of endophytic bacteria and physicochemical properties of rhizosphere soil ofCerasus humilis (Bge.) Sok. introduced for the control of rocky desertification in the karst graben basin with different years were studied. [Results] Planting years ofC.humilis had a direct and significant influence on the rhizosphere soil quality and an indirect effect on the bacterial community in the roots. The endophytic bacterial community was mainly characterized by symbiotic interactions. The top three dominant bacterial genera identified by the co-occurrence network in the first year and third year wereStreptomyces,Burkholderia-Caballeronia-Paraburkholderia andChitinophaga, and the top three dominant bacterial genera in the fifth year wereStreptomyces,Chitinophaga and Haliangium, which had biocontrol effects. The endophytic bacterial community was shaped by stochastic ecological drift processes. [Conclusion] The differences of endophytic bacterial communities along the planting year gradient are due to the microbial diversity endowed by stochastic processes. The interactions among endophytic bacteria and the dominant bacteria with biocontrol effects could promote the colonization and growth ofC.humilis, thereby enhancing the ecological and economic benefits ofC.humilis for the comprehensive control of rocky desertification in the karst graben basin.