Abstract: This study aims to explore the effect of low-temperature storage on the color change of Huping jujube. The natural half-red Huping jujube was taken as the raw material and then stored at 0°C (0±1°C) low temperature, while setting 18 °C (18±2°C) room temperature storage as control. A series of experiments were carried out to explore the color mechanism of Huping jujube. Therefore, the physiological and biochemical indexes were monitored to determine the combination of pigment and browning, including the color difference (L, a, b, and △E), chlorophyll, total phenols, total flavonoids, proanthocyanidins, soluble sugar content, and polyphenol oxidase (PPO) activity. The samples were selected for transcriptome sequencing. The results showed that the state of low-temperature storage Huping jujube was significantly better than that of normal-temperature storage. The color of the jujube fruit peel gradually deepened with the extension of storage time, and the chlorophyll was degraded continuously. The contents of total phenols, total flavonoids, and soluble sugar decreased gradually, indicating that the transformation of fruit color was related to its tissue oxidation. The gradual increase of PPO activity accelerated the consumption of total polyphenols in tissues. The transcriptome analysis showed that the differential genes annotated by GO were concentrated mainly in the cellular component (CC) and molecular function (MF). The differentially expressed genes related to color were concentrated in the biological process (BP); The pathways annotated by KEGG were closely related to Porphyrin and chlorophyll metabolism, Flavonoid biosynthesis, and metabolism. A total of 18 differentially expressed genes with high expression levels were further screened. Among them, the expression levels of trans-cinnamate 4-monooxygenase gene (LOC107411586, LOC107417662), flavonol synthase gene (LOC107415994), flavonoid 3',5'-hydroxylase 1-like gene (LOC107403962) were up-regulated, whereas, the expression level of chalcone isomerase-like protein 2 gene (LOC107413997) was down-regulated. The expression levels of the porphobilinogen deaminase gene (LOC107405622), uroporphyrinogen-III synthase gene (LOC107420915), uroporphyrinogen decarboxylase gene (LOC107413960), oxygen-dependent coproporphyrinogen-III oxidase gene (LOC107416652), magnesium-chelatase subunit Chll gene (LOC107411201), magnesium-chelatase subunit ChlH gene (LOC107431688), magnesium protoporphyrin IX methyltransferase gene (LOC107407353), magnesium-protoporphyrin IX monomethyl ester oxidative cyclase gene ( LOC107423584 ), protochlorophyllide reductase gene (LOC107432449), and glutamate-tRNA ligase gene (LOC107411689) were all down-regulated. Trans-cinnamate 4-monooxygenase gene (LOC107411586, LOC107417662), flavonol synthase gene (LOC107415994), and flavonoid 3',5'-hydroxylase 1-like gene (LOC107403962) were involved in the oxidation-reduction as the key genes for the biosynthesis of flavonoids. The flavonoid 3',5'-hydroxylase 1-like gene (LOC107403962) was a key gene for anthocyanin synthesis. The up-regulation of its expression led to the up-regulation of the expression of dihydroquercetin, the precursor of anthocyanin synthesis, leading to the content of anthocyanin. The chalcone isomerase-like protein 2 gene (LOC107413997) was a key gene for the biosynthesis of polyphenolic compounds. The down-regulation of its expression led to the down-regulation of the precursor of polyphenolic compounds, which ultimately dominated the content of polyphenolic compounds. The protochlorophyllide reductase gene (LOC107432449) was involved in the metabolic process as the key gene for chlorophyll synthesis. The down-regulation of its expression directly dominated the biosynthesis of chlorophyll a. At the same time, the expression of differential genes in the chlorophyll synthesis metabolic pathway was down-regulated, and the expression of most differential genes related to anthocyanin synthesis showed an upward trend, indicating that the content of chlorophyll and polyphenols decreased in the later stage of storage. The up-regulation of anthocyanin synthesis led to the color change of jujube fruit in the later stage of storage. This finding can provide a theoretical basis for the variation in the color quality of Huping jujube.