The Tibetan medicinal fruit E’seguo originates from two species, Malus toringoides (Rehd.) Hughes and Malus transitoria (Batal.) Schneid, both unique to the Hengduan Mountains. These species are predominantly found in high-altitude regions of Ganzi Prefecture, Sichuan Province, particularly in the Xianshui River and Yalong River basins. Malus toringoides (Rehd.) Hughes is far more abundant in both resource quantity and distribution compared to Malus transitoria (Batal.) Schneid. However, the nutritional and medicinal differences between the two remain unclear, which significantly impacts the development and utilization of E’seguo resources. This study aimed to measure the mineral content, nutritional components, and medicinal properties of E’seguo from 12 different regions of Ganzi Prefecture to explore the quality differences between these two species and across different regions. ICP-MS (Inductively Coupled Plasma Mass Spectrometry) was used to determine the mineral content, ultraviolet-visible spectrophotometry and potentiometric titration to analyze nutritional indicators, and HPLC (High-Performance Liquid Chromatography) to measure the medicinal components L-malic acid and 2-O-β-D-glucopyranosyl-L-ascorbic acid (AA-2βG). Results indicate that Malus transitoria (Batal.) Schneid contains higher levels of K, Ca, Zn, Mg, and Cu compared to Malus toringoides (Rehd.) Hughes, which has higher Fe and Mn content. Malus toringoides (Rehd.) Hughes from the Kangding and Litang regions showed the highest mineral content, with mineral elements primarily influencing polysaccharide levels, according to Mantel analysis. Nutritional and medicinal analyses revealed that Malus toringoides (Rehd.) Hughes outperformed Malus transitoria (Batal.) Schneid in all metrics except for the sugar-acid ratio. Given the mineral content and taste, Malus transitoria (Batal.) Schneid is better suited for consumption, while Malus toringoides (Rehd.) Hughes has superior medicinal properties, making it more appropriate for medicinal use. In the Malus transitoria (Batal.) Schneid regions, both Luhuo and Daofu are in the Xianshui River basin, with Daofu County producing the higher quality fruit. Among the nine Malus toringoides (Rehd.) Hughes regions, the M10 (Tuoba Township, Ganzi County) near the Yalong River had the highest overall score, followed by M7 (Yade Township, Luhuo County) and M6 (Keke, Xiala Tuo Town, Luhuo County), both of which are near the Xianshui River. In summary, Malus transitoria (Batal.) Schneid generally has higher mineral content, but Malus toringoides (Rehd.) Hughes has larger fruit and higher medicinal value, making the latter more suitable as a medicinal resource. At the same time, the medicinal quality of Xianshui River fruit was higher in the two watersheds of Malus toringoides (Rehd.) Hughes.