The aim of this study was to explore the regional characteristics of soluble sugars, organic acids, and stable isotopes (δ2H, δ18O, and δ13C) in Fuji apple and the viability of tracing the geographical origin. Totally, 181 Fuji apple samples from 2017 and 2018 from three main apple production regions in China, Bohai Bay (BHB), Loess Plateau (LP), and Northwest region (NW) were collected. The parameters of soluble sugars, organic acids, and stable isotopes in samples were analyzed with HPLC, IC, and IRMS, respectively. The results of regional difference analysis, multiway variance analysis, and correlation analysis indicated that sorbitol (Sor), glucose (Glu), fructose (Fru), sucrose (Sucr), δ2H, and δ13C can be used to distinguish the samples from the three regions. Stepwise linear discriminant analysis (SLDA) showed that the correct discriminant rate of samples from the advantageous production areas of apples in China (BHB and LP) was 82.2%, and the most effective indexes were Glu, Fru, Sucr, and δ2H. Moreover, satisfactory classification can be achieved in samples from BHB and NW, with a correct classification rate of 90.0%, and Sor, Glu, and Fru were included in the discrimination model. Furthermore, the validity of the discriminant model was verified by the prediction set. The study also found that organic acids were not suitable to distinguish the apple samples from the three regions. In addition, soluble sugars and stable isotopes could not effectively distinguish LP and NW samples, which was also the reason that the samples from the three main apple production regions could not be distinguished well.