Copper oxide nanoparticles (CuO NPs), as an antimicrobial nanomaterial, have found many applications in agriculture. Ubiquitous and complex root exudates (RE) in the plant root zone motivates the determination of how specific components of RE interact with CuO NPs. This work aims to reveal the role of maize (Zea mays L.)-derived RE and their components on the aggregation and dissolution of CuO NPs in the rhizosphere. We observed that RE significantly inhibited the aggregation of CuO NPs regardless of ionic strength and electrolyte type. In the presence of RE, the CCC of CuO NPs in NaCl shifted from 30 to 125 mM and the value in CaCl2 shifted from 4 to 20 mM. Furthermore, this inhibition was correlated with molecular weight (MW) of RE fractions. Higher MW fraction (>10 kDa) reduced the aggregation most. We also discovered that RE significantly promoted the dissolution of CuO NPs and lower MW fraction (<3 kDa) RE mainly contributed to this process. Additionally, phytotoxicity of CuO NPs in the presence of RE and different fractions of RE was evaluated. The addition of 20 mg/L RE reduced the seedlings growth rate to 1.89% after 7 days exposure to 25 mg/L CuO NPs, which were significantly lower than the control group (4.82%). Notably, Cu accumulation in plant root tissues was significantly enhanced by 20 mg/L RE. This study provides useful insights into the interactions between RE and CuO NPs, which is of significance for the safe use of CuO NPs-based antimicrobial products in agricultural production.