The rhizobiont can improve nutrient utilization efficiency and reduce soil-borne diseases through a cascade of plant-microbe-soil interactions, thereby maintaining the health of the soil-plant system. Developing green intelligent fertilizers based on this theory that target and regulate rhizosphere processes is a key breakthrough in achieving sustainable agricultural development. In the face of this challenge, this article focuses on the agricultural losses caused by nematode diseases and the ecological and environmental problems caused by chemical control. From a new perspective of the rhizobiont, it systematically explores new green control methods for soil-borne diseases driven by root exudates. The article first provided a detailed theoretical explanation of the rhizobiont, focusing on the key role of plant root exudates as a core driving force in shaping rhizosphere microbial communities, mediating multispecies synergistic interactions, and maintaining soil-plant health. Furthermore, it analyzed the molecular mechanisms by which different plant-derived functional substances recruit beneficial microorganisms and target the regulation of plant parasitic nematodes. Finally, the technical conception, product development, and effect verification of transforming these basic ecological principles into green intelligent fertilizer were further discussed. The key future research directions in this field in the future were prospected, thereby providing a practical example for the development of green intelligent fertilizer products based on the theory of rhizobiont, and providing an innovative theoretical and technical basis for the development of sustainable agriculture and food security.