Aims This study aimed to compare the effects of cold plasma (CP), ultraviolet (UV-C) and aqueous ozone (AO) on Botrytis cinerea and explore their application in preserving blueberry. Methods and Results The effects of CP, UV-C or AO on B. cinerea were investigated. Results showed that three treatments effectively inhibited the growth of B. cinerea, increasing cell membrane penetrability and causing the leakage of cytoplasm and nucleic acid. Scanning electron microscopy showed that CP caused the mycelium fold and collapse depression; UV-C caused the mycelium shrivelled; mycelium treated with AO appeared to fold and break. In the in vivo test in blueberry, all treatments effectively inhibited the growth of micro-organisms, maintained qualities and enhanced antioxidant activities in blueberry during postharvest storage. Conclusion Cold plasma, UV-C and AO effectively inhibited the growth of B. cinerea and significantly extended the shelf life of blueberry. Based on in vitro and in vivo tests, CP showed better effects to preserve blueberry compared with other treatments. Significance and Impact of the Study Our findings revealed the effective mechanisms of CP, UV-C and AO to inhibit B. cinerea in vitro. CP exhibited better application potential to preserve fresh fruit than traditional sterilization methods such as UV-C and AO.