Abstract: Interspecific interactions mediated by root exudates play an important role in biodiversity-ecosystem functioning (BEF) relationships. We reviewed and explained the advances in interspecific root-root interactions mediated by root exudates in agroecosystems with crop diversification, and highlighted the following: root exudates mobilize insoluble nutrients in the soil, facilitating the uptake of nutrients by the crop and neighboring plants; the increased accumulation of heavy metals by hyperaccumulating plants can reduce the accumulation of heavy metals in associated food crops; alteration of soil microbial community mediated by root exudates from one species can reduce the pathogens in the other crop species; root exudates, as signal substances, also play important roles in mediating the root-root recognition and plasticity response between species; for example, field weeds can be suppressed by root exudates from intercropped allelopathy plants with field crops. In addition, we highlighted some perspectives on practical applications and new methods of research on root exudates in crop diversification systems. These advances provide a theoretical basis for building sustainable agricultural ecosystems by matching the root secretions and signaling substances of different crop species, improving resource utilization, reducing pests and diseases through enhanced interspecific facilitation, and reducing fertilizer and pesticide inputs owing to suppression of weeds through allelopathic effects.