The objective of crop production is to harvest the photosynthetic products of crops. The harvest of these products reduces the amount of organic materials returned into the croplands, resulting in a decline in organic matter and available nutrient contents in farmland soil. Such characteristics of farmland production and the plant-soil feedback result in the unsustainable nature of farmland soil productivity. Therefore, it is crucial to implement appropriate countermeasures to sustain soil productivity. The application of chemical fertilizers addresses the issue of nutrient depletion in farmland soil and substantially enhances crop yield. Intensive agriculture, characterized by the high use of chemicals, achieves high crop yield, but also generally stimulates the activity of soil-borne pathogens. Consequently, the frequent occurrence of crop soil-borne diseases has become a bottleneck restricting the sustainable development of intensive agriculture. The existing studies have demonstrated a close association between aboveground biodiversity and soil microbial biodiversity, and plant-derived organic resource serves as the foundation for this relationship. Generally, soil-borne pathogens benefit more from crop root exudates than the antagonistic microbes. Monocropping in intensive agriculture leads to the simplification of available organic resources, resulting in a reduction in the biodiversity of active soil microbes, which further weakens soil suppressive ability against soil-borne pathogens. This paper proposes the addition of organic compounds during crop cultivation that can sustain the biodiversity of active soil microbes or enhance the activity of beneficial microbes, as an effective strategy to maintain soil biological health and suppress soil-borne diseases in intensive agriculture. To achieve this, it is crucial to investigate the organic compounds preferred by soil beneficial microorganisms and determine the optimal methods for organic amendment during crop growth.