The objective of this study was to investigate the effect of environmental factors (soil nutrition and meteorological factors) on fruit quality traits of ‘Fuji’ apples. ‘Fuji’ apple fruits, soil samples, and meteorological data were investigated from 66 commercial orchards covering 22 counties of the Loess Plateau region in China. Partial least squares regression (PLSR) and linear programming were combined to analyze the quantitative relationship between fruit quality and environmental factors. The effect of meteorological factors (55.99%) on fruit quality was greater than that of soil nutrition factors (44.01%) in the Loess Plateau apple-producing region of China. Optimum environmental factors for high-quality ‘Fuji’ apples in the Loess Plateau region were: soil organic matter (13.94–17.93 g ∙ kg−1), total N (0.77–1.03 g ∙ kg−1), available N (68.39–115.87 mg ∙ kg−1), P (62.39–124.67 mg ∙ kg−1), K (324.41–468.62 mg ∙ kg−1), Ca (6.54 mg ∙ kg−1), Fe (14.97 mg ∙ kg−1), Zn (1.55–2.72 mg ∙ kg−1), B (0.37 mg ∙ kg−1), and soil pH (7.98–8.20); mean annual temperature (18 ℃), total annual precipitation (431.2–713.8 mm), monthly mean temperature (19.9 ℃), lowest temperature (8.03 ℃), highest temperature (19.63 to 27.25 ℃), temperature difference between day and night (12.41 ℃), total precipitation (338.3–589.8 mm), relative humidity (56.57–82.41%), and sunshine percentage (36.96–55.87%) during the growing period (April–October).