Abstract: To elucidate the types of Gastrodia elata brown rot pathogenic fungi and the inhibitory effect of citral on them. Tissue isolation method, pathogenicity test, morphological observation and rDNA-ITS sequence analysis were employed to isolate and identify the pathogenic fungi using naturally-occurring G. elata as test material. Furthermore, the in vitro inhibitory effect of citral on the pathogenic fungi at different concentrations and its effect on the induced disease resistance of G. elata were investigated. Results demonstrated that the primary pathogenic fungi causing brown rot of Gastrodia elata were Trichoderma hamatum and Fusarium tricinctum. The inhibition rate against the pathogenic fungi exhibited a dose-dependent relationship with the concentration of citral, with an MIC value of 0.6 μL/mL. At 3 d post-inoculation, the diameters of the spots of Trichoderma hamatum and Fusarium tricinctum were 15.20 and 8.17 mm, respectively. It was determined that Trichoderma hamatum was the main pathogenic fungi causing brown rot of Gastrodia elata. Furthermore, the optimal control of Trichoderma hamatum was achieved by 0.6 μL/mL citral. The application of citral resulted in the accumulation of total phenolic and flavonoid contents, as well as the promotion of an increase in APX, PPO, POD, SOD and CAT enzyme activities in G. elata. This enhanced the resistance of postharvest G. elata to Trichoderma hamatum. The present study is of great significance for the control of brown rot pathogenic fungi of G. elata and the prolongation of its shelf life.