Abstract: In order to explore the effect of low temperature storage on the color change of Huping jujube, this experiment used natural half-red Huping jujube as raw material, stored at 0 °C (0°±1°) low temperature, and set 18 °C (18°±2°) room temperature storage as control to study the color change mechanism of Huping jujube. Therefore, the physiological and biochemical indexes were monitored, and the changes of color difference (L, a, b, △E), chlorophyll, total phenols, total flavonoids, proanthocyanidins, soluble sugar content and polyphenol oxidase (PPO) activity were determined in combination with pigment changes and browning process. 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. With the extension of storage time, the color of jujube fruit peel gradually deepened, and the chlorophyll was continuously degraded. 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. Through transcriptome analysis, it was found that the differential genes annotated by GO were mainly concentrated in the cellular component (CC) and molecular function (MF). The differentially expressed genes related to color were mainly concentrated in Biological process (BP); the pathways annotated by KEGG are mainly 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-cinnamic 4-monooxygenase gene (LOC107411586, LOC107417662), flavonol synthase gene (LOC107415994), flavonoid 3',5'-hydroxylase gene (LOC107403962) were up-regulated, and the expression level of chalcone isomerase gene (LOC107413997) was down-regulated. The expression levels of hydroxymethylbilane synthase gene (LOC107405622), uroporphyrinogen-III synthase gene (LOC107420915), uroporphyrinogen decarboxylase gene (LOC107413960), coporporphyrinogen-III oxidase gene (LOC107416652), magnesium-chelatase subunit I gene (LOC107411201), magnesium-chelatase subunit H gene (LOC107431688), magnesium protoporphyrin IX methyltransferase gene (LOC107407353), magnesium-protoporphyrin IX monomethyl ester oxidation gene (LOC107423584), protochlorophyllide reductase gene (LOC107432449), and glutamyl-tRNA synthetase gene (LOC107411689) were all down-regulated. Cinnamic acid 4-monooxygenase gene (LOC107411586, LOC107417662), flavonol synthase gene (LOC107415994), and flavonoid 3 ' -5 ' carboxylase gene (LOC107403962) are involved in the oxidation-reduction process and are key genes for the biosynthesis of flavonoids. The flavonoid 3 ' -5 ' carboxylase gene (LOC107403962) is a key gene for anthocyanin synthesis. The up-regulation of its expression leads to the up-regulation of the expression of dihydroquercetin, the precursor of anthocyanin synthesis, and ultimately affects the content of anthocyanin. The chalcone isomerase gene (LOC107413997) is a key gene for the biosynthesis of polyphenolic compounds. The down-regulation of its expression leads to the down-regulation of the precursor of polyphenolic compounds, which ultimately affects the content of polyphenolic compounds. The protochlorophyll reductase gene (LOC107432449) is involved in the metabolic process and is a key gene for chlorophyll synthesis. The down-regulation of its expression directly affects 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 leads to the color change of jujube fruit in the later stage of storage. This study can provide a theoretical basis for the change of color quality of Huping jujube.