Citrus fruits are rich in phenolic compounds that possess several health benefits. However, few studies have focused on the changes in phenolic compounds in citrus fruits during postharvest storage. This study dynamically monitored the phenolic content, components and antioxidant activity of ‘Tarocco’ blood oranges during a period of 12-week cold storage and on-tree storage, respectively. We investigated the alteration mechanism of phenolic compounds in blood oranges by evaluating phenylpropanoid pathway-related enzyme activities and gene expression. Results showed that flavanones were the main phenolic compounds in blood oranges. Both storage methods mainly stimulated the accumulation of phenolic acids to improve total phenolic content, which reached the maximum at week 12. Nonetheless, blood oranges had a higher phenolic content and antioxidant activity under on-tree storage than cold storage. Furthermore, the enzyme activities and gene expression of the phenylpropanoid pathway demonstrated that the accumulation of phenolics in blood oranges during storage was highly related to the activation of the phenylpropanoid pathway. These results demonstrate that on-tree storage is a potential approach for extending the supply period of blood orange from the perspective of phenolic compounds.