Abstract Litchi is an important economic fruit in subtropical countries. The litchi downy blight (LDB) caused by the oomycete Peronophythora litchii severely affects the production and quality of litchi fruit, and is widespread in almost all litchi production regions of China. Therefore, there is an urgent need for effective and sustainable control strategies against LDB. Our previous study showed that Bacillus amyloliquefaciens LI24 and PP19, B. licheniformis HS10, B. pumilus PI26, and Exiguobacterium acetylicum SI17 are promising biocontrol agents (BCAs) in controlling LDB, and their volatile organic compounds (VOCs) could inhibit the growth of P. litchii in vitro. In this study, we found that pre-exposure of litchi fruit to VOCs produced by PP19, SI17 and PI26 can significantly reduce the severity of LDB during 36 h to 72 h post inoculation. We further analyzed VOCs produced from the three BCAs (i.e., PP19, SI17, PI26) by solid phase microextraction gas chromatography-mass spectrometry (SPME-GC–MS), and found that their chemical compositions varied substantially over incubation time and between BCAs. In total, 70, 98, 101 chemicals were detected in PP19, SI17, PI26 from 24 to 72 h of incubation, respectively; 17 of them were commonly produced at more than one time points by PP19, and 11 were selected for further study. Two of the compounds 1-(2-Aminophenyl)ethanone (EA) and Benzothiazole (BTH) showed inhibitory activity against both P. litchii on plates and LDB on litchi fruit when the compounds were directly applied, while another compound α-Farnesene (AF) was able to suppress LDB in vivo, but did not exhibit antagonistic activity against the pathogen in vitro, suggesting that it may act through induction of host defense mechanisms. Our results showed that the bacterial VOCs and compounds of BTH or AF could be promising for the control of LDB on harvested litchi fruit.