Taihu muskmelon, commonly known as “Laotaipo muskmelon” and “crisp muskmelon”, has a long history of cultivation. The skin of the muskmelon is white, the aroma is strong, the meat is crisp and sweet, and it is loved by consumers. However, there is a lack of research on the identification of the characteristics of Taihu muskmelon and the changes of metabolites during storage. The metabolites of Xiaobainiang, Yunaixiang 2 and Lüxiangtian were analyzed by ultra-high performance liquid chromatography-high resolution mass spectrometry. At the same time, the Xiaobainiang was stored at room temperature for 1 d and 8 d, and the metabolites of its flesh were analyzed. Using common muskmelon varieties in the market, Lüxiangtian and Yunaixiang 2, as controls, a total of 18 136 metabolites were identified in the flesh of the three muskmelon varieties, Xiaobainiang, through metabolomics analysis, which was higher than the control of 14 879 metabolites in Lüxiangtian and 15 943 metabolites in Yunaixiang 2. Among them, a total of 1 902 unique metabolites were identified in Xiaobainiang, which was higher than the 449 unique metabolites in the control group of Lüxiangtian and 542 unique metabolites in Yunaixiang 2. Analysis of the content of metabolites revealed that the flavonoid compound kaempferol-3-gentiobioside in Xiaobainiang was significantly higher than that in Lüxiangtian and Yunaixiang 2, which were 136 and 3 200 times higher, respectively. Meanwhile, the metabolites of Xiaobainiang muskmelon were measured after being stored at room temperature for 1 and 8 days, and principal component analysis (PCA) was performed on the differential metabolites. The results showed that there were no significant differences in the differential metabolites. In conclusion, Xiaobainiang not only has a certain level of storage stability, but also contains a high amount of flavonoid compounds, particularly kaempferol-3-gentiobioside, which can serve as a characteristic marker for identifying Taihu fragrant melon Xiaobainiang. This study is of significant importance for the identification and promotion of Xiaobainiang.