The work aims to explore the effects of different modified atmosphere packaging (MAP) bags on the appearance quality and physiological and biochemical indices of manaohong cherries (Prunus pseudocerasu L.) during storage. Manaohong cherries were packaged with different MAP bags and stored at (1±0.3) °C for 21 d. The relevant indices of the cherries were measured every 7 d to study the changes in quality within the MAP bags during storage and to identify the optimal storage packaging conditions. As the storage period extended, storage in PE packaging effectively reduced the fruit decay rate, suppressed the increase of respiration rate and soluble solids content (TSS), and maintained high fruit hardness, thus improving fruit quality and nutritional value. Specifically, PE20 packaging significantly delayed the decline in vitamin C and polyphenol content, inhibited the accumulation of malondialdehyde (MDA), and maintained high peroxidase (POD) activity. Additionally, principal component analysis (PCA) composite scores indicated that PE20 packaging exhibited the best overall effect during the storage of manaohong cherries. During the low-temperature storage of manaohong cherries, PE20 packaging is the most effective in maintaining the storage quality of the fruit.