Abstract: The nutritional quality of Fuji apple candy, acid, and polyphenols varies among production areas in China, so the construction of its origin traceability technology is beneficial to the implementation of production area protection, characteristic product fidelity and sustainable industrial development. Therefore, 18 nutritional quality indexes such as total carbohydrate, acid and polyphenols of Fuji apple from six production areas, namely, Aksu in Xinjiang, Jingning in Gansu, Luochuan in Shaanxi, Lingbao in Henan, Yantai in Shandong and Zhaotong in Yunnan were tested and analyzed in this paper. And effective origin traceability nutritional quality indicators were screened based on multivariate statistical analysis to construct a method for the identification of different origins of Fuji apple. The discriminative model for the identification of different production areas of Fuji apple was constructed. The results showed that compared with other production areas, the contents of Aksu Fuji apple total carbohydrate and sorbitol were high, the contents of Jingning Fuji apple total phenols and chlorogenic acid were high and the contents of Lingbao Fuji apple catechin and phloretin were high. The contents of Luochuan Fuji apple fructose and phlorizin were high, the contents of Yantai Fuji apple sugar-acid ratio and rutin were high, the contents of Zhaotong Fuji apple quercitrin and epicatechin were high. The fruit indicators measured were subjected to orthogonal partial least squares discriminant analysis with a Q² value of 0.794, a matrix R²X value of 0.885 and a differentiation parameter R²Y value of 0.874, and a valid OPLS-DA appellation identification model with a correct discrimination rate of 93.33% was established. The linear discriminant was used and eight valid indicators including V_C, sorbitol, catechin, quercetin glycoside, quercetin rhamnoside, quercitrin, rutin and quercetin were screened and obtained, which could distinguish 100% of Fuji apple in each appellation. Fruit sugar accumulation in each appellation was closely related to the appellation environment. Total carbohydrate and total acid content were significantly and negatively correlated with rainfall, and sucrose content was significantly and positively correlated with temperature difference. This study was expected to provide technical support for the development of Fuji apple industry and the protection of geographical indication products in China.