The study first demonstrated that burdock fructooligosaccharide (BFO) could inhibit peel browning in green banana, with 0.5% BFO treatment showing the most significant suppression of peel browning during low-temperature storage (7 ± 1 °C). The results revealed that 0.5% BFO treatment effectively restrained the increase in electrolyte leakage and malondialdehyde (MDA) content and maintained cell membrane integrity. Furthermore, BFO treatment enhanced total phenolic content and antioxidant capacity, alleviated oxidative damage, and better preserved the external quality of banana peel. Simultaneously, BFO treatment markedly inhibited both the activities of chlorophyll-degrading enzymes and their relative gene expression levels in banana peel, thereby maintaining higher chlorophyll content. This research provided a new insight into the mechanism of inhibiting peel browning for low-temperature storage preservation of banana.