During the processing of longan juice, product quality is often compromised by undefined varietal characteristics and the use of multiple raw material varieties. To investigate the differences in storage quality among varieties after heat sterilization, the changes in physicochemical indicators and nutritional components of four main varieties—‘Qiuxiang’, ‘Chuliang’, ‘Shixia’, and ‘Gaobao’—were compared during storage following heat sterilization. The results indicate that ''Qiuxiang'' juice had the highest degree of browning and the lowest ascorbic acid content before storage, and by the 8th day of storage, it was no longer detectable, with a loss rate approaching 100%. During storage, the browning degree and color difference of the longan juice of the four varieties showed an increasing trend. Among them, the browning degree of ''Gaobao'' juice increased the most, reaching 2.11 times the initial value by the end of storage, with a △E of 11.29.. At the end of storage, ‘Chuliang’ juice exhibited the highest loss rate of ascorbic acid (79.34%), while ‘Shixia’ juice showed the lowest loss rate of total phenols (17.62%). The contents of reducing sugar, total sugar, and soluble solids remained essentially stable, whereas the 5-hydroxymethylfurfural (5-HMF) content generally increased, although it remained relatively stable in ‘Shixia’ juice during the later stages of storage. Principal component analysis revealed that the quality change trends of ‘Gaobao’ and ‘Chuliang’ juices were relatively similar. Correlation analysis indicated that the browning degree and color difference of ''Gaobao'' juice were highly significantly negatively correlated with ascorbic acid and total phenols, and showed no correlation with reducing sugars. In summary, ''Qiuxiang'' juice has the highest browning degree throughout the storage period and is not suitable for longan juice product processing; ''Gaobao'' juice has relatively good initial color, but browning increases rapidly during storage, with poor color stability; compared with ''Shixia'', ''Chuliang'' juice has good initial color and low browning at the end of storage, suitable for short shelf-life products, while ''Shixia'' juice maintains better color stability during storage, making it suitable for long shelf-life longan juice processing. This study provides a theoretical basis for evaluating the storage quality of longan juice from different varieties and for the selection of raw material varieties.