[Background] Siderophores is considered as a new bioactive substance with development and utilization value, and has been gradually applied to the control of plant pathogens. [Objective] To clarify the optimal fermentation conditions for the production of siderophores by rhizosphere growth-promoting bacteria Rahnella aquatilis JZ-GX1 and further explore the potential role of siderophores in controlling plant root diseases. [Methods] Several fermentation factors affecting the secretion of siderophores were studied by CAS fermentation analysis, and the antagonistic effect of siderophores on two forest pathogenic fungi was determined by mycelial growth inhibition rate method. [Results] The results showed that KMB-based medium, initial pH 8.0, liquid volume 25 mL/50 mL, inoculated with 1%, and cultured at 28 °C for 36 h, can obtain higher yield of siderophores; it can produce carboxylate and hydroxamic acid type siderophores; under optimal conditions, the inhibition rate of the fermentation stock solution against Phytophthora cinnamomi and Rhizoctonia solaniwas were 100%. [Conclusion] Rahnella aquatilis JZ-GX1 has a good potential for controlling root diseases of forest trees in alkaline soils.