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Cold storage is one of the most commonly used ways to store pomegranates (Punica granatum L.). Husk browning can occur during cold storage due to phenolic metabolism and energy decay. Three pomegranate cultivars grown in Shaanxi: the introduced cultivar ‘Tunisia soft seed’, the traditional cultivar ‘Jingpitian’ and the newly bred cultivar ‘Lishanhong’ were used to explore the relationship between husk browning and phenolic and energy metabolism under storage conditions of (4.0 ± 0.5) ℃ and 85%–90% relative humidity, and the storage characteristics of these cultivars were compared. The results showed that with the extension of storage time, browning index increased, 1,1-diphenyl-2-picryl-hydrazyl (DPPH) radical scavenging capacity increased at first and decreased later, 2,2’-azino-bis-3-ethylbenzothiazoline 6-sulfonic acid (ABTS) cation radical scavenging capacity, total phenol and flavonoid contents fluctuated only slightly, and anthocyanin content increased at first and then decreased for all cultivars. Among them, the contents of total phenols, total flavonoids and anthocyanins were highest in ‘Tunisia soft seed’ pomegranates. During storage, polyphenol oxidase (PPO) activity remained lowest, and phenylalanine ammonialyase (PAL) activity remained highest in ‘Tunisia soft seed’ pomegranates. Peroxidase (POD) activity was always highest in ‘Jingpitian’ pomegranates. In addition, ‘Tunisia soft seed’ pomegranate husk maintained higher adenosine triphosphate (ATP) and adenosine diphosphate (ADP) contents and energy charge, as well as higher Mg2+-ATPase and H+-ATPase activities during storage. The correlation analysis showed that the browning index of ‘Jingpitian’ pomegranate husk, which was highest among the three cultivars, was significantly positively correlated with total phenol and flavonoid contents, POD and PAL activities, and ATP and ADP contents (P < 0.05 and P < 0.01); the browning index of ‘Tunisia soft seed’ pomegranate husk, which was lowest, was significantly positively correlated with POD activity and the content of adenosine monophosphate (AMP) (P < 0.01); and the browning index of ‘Lishanhong’ pomegranate husk, which was in the middle, was significantly positively correlated with total phenol and AMP contents (P < 0.05 and P < 0.01, respectively) but significantly negatively correlated with Mg2+-ATPase activity (P < 0.01). Principal component analysis (PCA) showed significant quality differences between ‘Tunisia soft seed’ pomegranates and the two other cultivars. The above findings demonstrated that the browning degree of pomegranate husk under cold storage conditions varied among cultivars and was related to phenolic and energy metabolism.