Winter jujube (Ziziphus jujuba Mill. cv. Dongzao) is a very popular horticultural fruit worldwide, which contains a high number of bioactive compounds. Nevertheless, jujube is perishable by microbial contamination and has a short shelf life under non-controlled conditions. Cold atmospheric plasma (CAP) presents a great potential for food sterilization, maintain postharvest quality, and prolonged storage time. Herein, this study investigated the potential effect of CAP with different exposure times (0, 5, 10, and 20 min) on the physicochemical and biochemical changes in jujube during 15-day storage at 4°C and 90% relative humidity (RH). The results showed that CAP treatment could obviously delay ripening, but displayed no effects on the speed of weight loss and moisture content. Meanwhile, the total native aerobic bacterial count in each jujube group was restrained during whole storage. However, CAP treatment showed a time-dependent manner to improve gene expression (PAL, 4CL, DFR, ANS, LAR, and ANR) related to phenolic biosynthesis. As compared to other groups, 20-min CAP treatment can keep or increase total phenolic content (TPC), maintain antioxidant activity, and reduce oxidative damage. Furthermore, the hydrogen peroxide (H2O2) and malondialdehyde (MDA) content in jujube during middle storage were visibly reduced by 20-min CAP treatment. All in all, our findings concluded that appropriate CAP exposure time can be a promising candidate for the postharvest preservation of jujube.