The harm caused by chemical fertilizers to soil environments and plants has become a global issue, impacting agricultural productivity and sustainability. The use of microbial organic compound fertilizers has demonstrated significant potential in improving soil conditions and enhancing land productivity. However, the effects of different fertilization types and amounts on the physicochemical properties of rhizosphere soil, soil microbial communities, root microbial communities, and crop quality, as well as the regulatory mechanisms by which key strains influence plant quality, remain unclear.