Fresh‐cut fruits were convenient for consumers but vulnerable to quality deterioration, including browning, softening, and volatile aroma loss. In this study, the whole nectarines were pretreated with 100% O2 (pure oxygen, PO) for 2 h and stored at near‐freezing temperature (NFT, −1.5 ± 0.1°C) for 9 days after cutting. We investigated the changes of samples in browning degree, enzyme activity, cell membrane permeability, antioxidant activity, and aroma components. Specifically, PO pretreatment increased the peroxidase (POD) and phenylalanine ammonia‐lyase (PAL) activities, which endows the whole nectarines with resistance to environmental stresses before fresh‐cut. NFT storage effectively inhibited the activity of the polyphenol oxidase (PPO) and the increase of the total phenolic content (TPC). Higher antioxidant levels and anti‐browning effects were observed in fresh‐cut nectarines treated with PO + NFT, which demonstrated by higher levels of 2,2‐diphenyl‐1‐picrylhydrazyl (DPPH) free radical scavenging capacity, ferricion reducing antioxidant power (FRAP), and enzyme activity ratios (ratio 1 and ratio 2). During the storage of 9 days, the firmness and membrane permeability were preserved, malondialdehyde (MDA) content was suppressed, which delayed the softening of nectarine tissue. Furthermore, soluble solids content (SSC) and titratable acid (TA) were also well preserved by PO + NFT, which maintained the physiological and metabolic qualities. Electronic nose tests revealed that PO + NFT postponed the volatile aroma deterioration. In conclusion, PO + NFT effectively maintains the storage quality of fresh‐cut nectarines.