Atemoya (Annona cherimola × A. squamosa) is a subtropical climacteric fruit and has excellent flavor and nutritional value. However, the shelf life of atemoya is limited because it is very susceptible to soften after harvesting and easily suffers chilling injury in low temperature. Currently, changes in the quality traits of atemoya and their correlations during post-ripening at typical storage temperatures have not been clarified. In this study, atemoya was respectively stored at 25 ℃ and 15 ℃ (85 ± 5% RH) for 5 d and 10 d, then the cell morphology and specific fruit qualities were investigated using optical microscopy, low-field nuclear magnetic resonance, and texture analysis etc., to reveal the mechanisms underlying ripening. The results showed that the weight loss of atemoya was respectively up to 13.18 ± 0.55% and 7.62 ± 0.52% on the last day of storage at 25 ℃ and 15 ℃. Starch completely degraded within 2 d and reducing sugars reached the maximum level of 150.93 ± 8.26 g·kg⁻¹ on day 3 at 25 ℃, while at 15 ℃, the starch completely degraded within 5 d and reducing sugars showed a continuous upward trend and reached the maximum level of 143.88 ± 15.50 g·kg⁻¹ on day 10. Additionally, at both temperatures, atemoya showed a trend of parenchyma loosing, pectin degradation, soluble solids accumulation and water status changing during storage. Principal component analysis and correlation analysis showed that changes in the moisture status had a more important impact on postharvest behavior at 25 ℃ while the accumulation and consumption of reducing sugars had a more important impact at 15 ℃. This study provides insights on the correlations and differences in fruit ripening quality characteristics under different environmental temperatures. It also provides recommendations for economically viable and energy-efficient methods of preserving fruit quality.