The aroma, taste, and flavour profiles of mango cultivars vary, directly influencing their marketability and consumer acceptance. In this study, we explored the effects of volatile organic compounds (VOCs) on the distinct aromas of two mango cultivars during storage using GC-IMS and HS-SPME-GC-MS combined with OPLS-DA analysis. Our findings revealed that the terpene and aldehyde contents were higher in the ‘Tainong’ mango cultivar, compared to the ‘Hongyu’ mango, while the ester content was lower. The aroma was attributed to the presence of terpinolene, 2-nonenal, delta-carene, and alpha-phellandrene in the early stages of storage, and later—between 5 and 11 days—to ethyl acetate, ethyl butyrate, and ethyl propanoate. Further analysis of characteristic VOCs using OPLS-DA demonstrated and explained the strong grassy aroma of the ‘Tainong’ mango, and the strong fruity and sweet aromas of the ‘Hongyu’ mango. Additionally, esters mainly accumulated during the later periods of storage, especially propyl butyrate, which was produced and accumulated when fruit quality deteriorated in the later storage period. Our study provides a theoretical basis for detecting mango VOCs during storage to determine the appropriate marketing time for the two mango cultivars and enables informed consumer choice.