AbstractIn order to study the effect of volatile organic compounds (VOCs) produced by Bacillus subtilis CF‐3 combined with heat treatment on Monilinia fructicola in peach and Colletotrichum gloeosporioides in litchi fruit, fruits were treated with B. subtilis CF‐3 VOCs and hot air alone or in combination. The quality indexes of peach and litchi fruit after treatment and the changes in defense‐related enzymes were measured. The results showed that the B. subtilis CF‐3 VOCs combined with heat treatment could significantly reduce the rot index of peach and litchi fruit, and effectively maintain firmness and soluble solids content, as well as reduce weight loss of fruits. The combined treatment effectively enhanced the activity of peroxidase (POD), polyphenol oxidase (PPO), catalase (CAT), and superoxide dismutase (SOD) than either treatment alone, and enhanced the resistance of fruit to pathogenic fungi by activating disease‐resistant enzymes (phenylalanine ammonia‐lyase [PAL], chitinase [CHI], β‐1, 3‐glucanase [GLU]) activity. In this study, B. subtilis CF‐3 VOCs combined with heat treatment maintained the quality and delayed the decline of peach and litchi fruit, providing a theoretical basis for future applications.Practical ApplicationThe combination of B. subtilis CF‐3 VOCs and heat treatment reduce the extent of M. fructicola and C. gloeosporioides. The combination maintain the quality of peach and litchi better. The combination obviously improve the activity of defense‐related enzyme in fruit.