This study is intended to clarify the role and mechanism of microbial agents in alleviating continuous cropping obstacles in apple orchards. A combination of pot experiments, high-throughput sequencing, and bioinformatics analysis was conducted to investigate the effects of soil remediation microbial agents and Trichoderma harzianum agent on apple seedling growth and the rhizosphere soil microbial community. The results showed that in continuous cropping apple orchard soil, inoculation with the soil remediation microbial agents significantly enhanced the SPAD value of apple seedling leaves, and rose by 12.15% when it compared with CK1. The inoculation of both soil remediation microbial agent and Trichoderma harzianum agent were more favorable to apple seedling growth than CK1. The application of soil remediation microbial agent and Trichoderma harzianum increased the apple seedling index by 146.51% and 25.58%, respectively. Meanwhile, total root length, total root surface area, average root diameter, total root volume, and root tip number were raised by 123.20% and 35.50%, 146.34% and 42.25%, 9.55% and 5.10%, 178.95% and 48.37%, 136.06% and 22.12%, correspondingly. Apple orchards which inoculated with the soil remediation microbial agents and Trichoderma harzianum agent significantly enhanced the phylogenetic diversity of bacterial communities in the rhizosphere soil while reducing the diversity and evenness of fungal communities. Inoculation with these two agents, the relative abundance of Trichoderma species was significantly higher than three control treatments, whereas the relative abundance of Fusarium species were decreased. Trichoderma and Fusarium species were key factors to the differences in the fungal community structure of rhizosphere soil. The relative abundance of Pyrinomonas was significantly lower in the two inoculated treatments compared to CK1. The soil remediation microbial agent treatment significantly decreased the relative abundance of Luteitalea while increasing the relative abundance of Luteitalea pseudomonas, whereas the Trichoderma harzianum agent treatment significantly increased the relative abundance of Lysobacte. Pyrinomonas, Luteitalea, Pseudomonas and Lysobacte were identified as important species driving differences in the bacterial community structure of rhizosphere soil. In conclusion, the application of the soil remediation microbial agent and Trichoderma harzianum agent in continuous cropping apple orchard soil substantially enhanced the microbial structure and function of the rhizosphere soil, benefited apple seedling growth.