Postharvest fungal diseases in fruits not only cause significant economic losses but also severely constrain the development of the fruit industry. Compared with chemical pesticides, fumigation using volatile organic compounds (VOCs) demonstrates superior safety and efficacy due to their non-direct contact mechanism with fruits. Therefore, identifying compounds with highly effective antifungal properties holds crucial application value. Here, VOCs produced by Burkholderia sp. NAU16 demonstrated remarkable inhibitory effects on the growth of multiple phytopathogenic fungi, with the most pronounced antifungal activity observed against Penicillium digitatum. The inhibition rates for mycelial growth and spore germination reached 80.9 % and 89.7 %, respectively. The compositional analysis of VOCs was conducted using SPME-GC-MS, and Dimethyl trisulfide (DMTS) exhibited the strongest antifungal activity, with a minimum inhibitory concentration (MIC) of 0.103 mL/L. Treatment with DMTS caused severe disruption of the fungal cell wall structure, along with significant ROS accumulation and DNA fragmentation, suggesting that apoptosis may be triggered in the affected cells. At a concentration of 2 × MIC, DMTS significantly inhibit the infection of P. digitatum on citrus within 7 days. Finally, the metabolic changes of citrus after DMTS fumigation were analyzed, and found that DMTS could enhance the suppression of fungal infection by promoting flavone and flavanol biosynthesis.