Abstract Continuous cropping obstacles (CCOs) constitute a major threat to agricultural productivity and environmental quality. Despite the recognized significance of rhizosphere restoration for CCOs, the mechanisms underlying rhizosphere restoration are not well understood. We conducted a pot experiment by planting Panax notoginseng with the addition of biochar, plant ash, the combination of biochar and plant ash (biochar:plant ash=4:1) or without any addition of biochar and plant ash. We found that rhizosphere soil with planting P. notoginseng, without any addition of biochar and plant ash, had a more homogeneous fungal community structure than soils added either with biochar, plant ash or the combination of biochar and plant ash. Among all treatments, the rhizosphere soil added with the combination of biochar and plant ash had the highest fungal and bacterial alpha-diversity. The combination of biochar and plant ash addition also enriched AMF Rhizophagus (TOP3 diff genus) in the rhizosphere soil compared to that without any biochar and plant ash addition. The co-occurrence network analysis demonstrated that Rhizophagus assembled a core microbial functional circle which helped suppress pathogens by promoting competition for amino acids and improving phenolic acid utilization, nutrient availability, and soil pH. Moreover, the metabolomic analysis revealed that the rhizosphere soil with the combination of biochar and plant ash addition upregulated the phenylalanine-tyrosine-tryptophan biosynthesis pathway, resulting in a decline of phenolic acid production and an increase amino acid accumulation in comparison with that without any biochar and ash addition (OPLS - DA, VIP > 1, FC ≥ 2, FC ≤ 0.5). Our results highlighted the importance of the interplay among keystone microbial species, pH and key metabolites in the rhizosphere soil in mitigating CCOs, building a framework for developing effective management for CCOs. Graphical Abstract