Abstract: Whole-genome genetic analysis, somatic variation detection, and fruit quality evaluation were performed on different ‘Changshanhuyou’ (Citrus × aurantium L.). specimens. Results showed that Changshanhuyou clustered with the original sour orange cultivars used in Aurantii Fructus production, such as Huangpi (C. aurantium L. ‘Huangpi’), Daidai (C. aurantium L. ‘Daidai’), Chuluan (C. aurantium L. ‘Chuluan’), and Tangcheng (C. aurantium L. ‘Tangcheng’), exhibiting 76.99%–91.06% genetic similarity with sour orange (C. aurantium L.). Fruit quality fluctuated and somatic mutations increased with age of the Changshanhuyou trees. Fruit quality was not influenced by the use of trifoliate orange (Poncirus trifoliata (L.) Raf.) as the rootstock, but higher somatic mutations were detected in the grafted trees. The mutated genes were mainly involved in senescence repair and stress defense. In conclusion, this study confirmed that Changshanhuyou is a domesticated form of sour orange, demonstrating stable fruit quality and genetic material within its optimal production period. This work provides a theoretical basis for the promotion of Changshanhuyou and grafting.