Abstract: With consumers' increasing awareness of food safety and health demands, organic food has gained widespread attention globally．Although China's organic agriculture started relatively late, it has developed rapidly．As an important category of certified organic products, Fuji apples have not yet been systematically evaluated for their quality characteristics．Therefore, a comparative analysis of physicochemical quality indicators and metabolites between Fuji apples from certified organic production systems and conventional production systems was conducted．Quality indicator test results showed that organic apples significantly outperformed conventional apples in terms of firmness, soluble solid content, and titratable acidity, while there was no significant difference in vitamin C content between the two．Non-targeted metabolomics analysis identified a total of 21 differential metabolites, primarily including quercetin, cyanidin-3-glucoside, and α-linolenic acid derivatives．These compounds, dominated by phenolic compounds and specific fatty acids, can serve as potential biomarkers for distinguishing apples from two production systems．Multidimensional evidence confirms that of organic production system have a positive regulatory impact on apple quality, offering a scientific basis for quality certification, market promotion, and production practices of organic apples．