To predict the quality of Fuji apples, this study investigated the characteristics and correlations of their fruit quality according to storage method and storage period. Fuji apples were stored in cold storage at 0oC for 250 days with no treatment, with 1-MCP treatment, and under controlled atmosphere (CA) storage. According to the storage method, the weight loss was the lowest in the CA-treated group (3.43%) until 250 days, and the change in fruit firmness was the least in the 1-MCP group. The titratable acidity remained above 0.2% for 1-MCP and CA storage until 250 days and decreased to 0.1% for cold storage. The principal component analysis showed a difference in quality between the 1-MCP group, CA group, and cold storage group after 200 days of storage. Six types of volatile components were commonly detected in all storage methods, while three types of independent components with a low threshold were detected in 1-MCP. Weight loss, titrable acidity, and firmness were highly correlated with physicochemical quality, and CA storage was judged to be a long-term storage technology that satisfies consumers’ tastes by maintaining excellent flavor and quality.