In this study, we investigated the effects of volatile organic compounds (VOCs) produced by Bacillus subtilis CF-3 on the growth and development of Colletotrichum gloeosporioides and evaluated the elicitation of active defense responses in harvested litchi fruits. In vitro experiments were conducted to explore the bacteriostatic effect of VOCs in inhibiting pathogenic fungi by means of plate enthalpy test, scanning electron microscopy, transmission electron microscopy, and gas chromatography-mass spectrometry (GC-MS). The results showed that 2,4-di-tert-butylphenol and CF-3 24-h fermentation broth (24hFB) can significantly inhibit the germination of fungal spores, disrupt hyphal and cell morphology, and decrease cell membrane fluidity and integrity, resulting in the changes of indexes. In addition, the bacteriostasis of VOCs in the defensive ability of litchi fruits to C. gloeosporioides was studied, and it was shown that 2,4-di-tert-butylphenol and CF-3 24hFB can inhibit the activity of the pathogenic enzymes (pectinase and cellulase) secreted by C. gloeosporioides to reduce the decomposition of plant tissues, activate antioxidant enzymes (peroxidase, polyphenol oxidase, catalase, and superoxide dismutase) in the fruit to eliminate excessive reactive oxygen species in fruits in order to reduce plant cell damage and activate disease resistance enzymes (phenylalanineammonialyase, chitinases, β-1,3-glucanase) to enhance the resistance of litchi fruits to C. gloeosporioides and inhibit its growth. This study investigated the bacteriostasis of VOCs in inhibiting C. gloeosporioides and inducing the resistance of litchi fruits, providing a theoretical basis for future applications.