Five Xinjiang apple local resources with different colours of skin and flesh, Kizi Alma, Kara Alma, Ak Alma, Ili Wild Apple and Lemon Begonia, were selected for quality refinement evaluation by four indicators of fruit appearance quality, inner quality, nutritional quality and aroma quality, and the expression of genes related to the anthocyanin synthesis pathway in the flesh of redfleshed apples was investigated. The differences between different fruit quality indicators of local apple resources in Xinjiang were clarified to provide information for the rational use of local apple resources in Xinjiang. The results showed that: (1) all the five featured resource varieties were medium and smallfruited apples, among which the redfleshed Kizi Alma had better appearance quality than the cultivar Fuji, while Lemon Begonia had the lowest appearance quality index. (2) The sugar and acid contents of Ak Alma was significantly lower than that of Fuji, while the acid content of Lemon Begonia was higher than that of Fuji and other varieties. (3) The flesh hardness of Ili Wild Apple was significantly higher than that of Fuji, while the flesh hardness of the redfleshed resource varieties were all lower in flesh hardness than that of Fuji, with flabby flesh and less resistance to storage and transportation, while they were the richest in total phenols and flavonoids and had the strongest antioxidant capacity, all significantly higher than that of cultivar Fuji. (4) In terms of aroma quality, the redskinned resource Kara Alma contained the richest variety and content of volatile substances, with its content nearly twice that of the lowest cultivar Fuji, and the redfleshed resource had the lowest contents of volatile substances. The volatile substances of the red flesh resources were dominated by alcohols, while the red skin resources Cara Alma, Ili Wild Apple and Lemon Begonia were dominated by aldehydes. (5) Principal component analysis showed that the overall quality performance of each Xinjiang apple local resource in terms of nutrition and aroma quality was: KZARM > KLARM > AKARM > FS > YLYPG > NMHT. (6) The expression of genes related to the anthocyanin synthesis pathway in the flesh of red flesh apples indicated that the key gene in the process of flesh anthocyanin accumulation was UFGT.