Lycium barbarum L. (abbreviated to L. barbarum) is a traditional medicinal and edible plant cultivated in different ecological areas in China. In this study, “Ningqi” No.1, one of the main cultivars of L. barbarum, was collected from 10 different important cultivation areas in 5 autonomous regions or provinces of China. Partial least squares regression and correlation analysis were used to analyze the relationship between 16 ecological factors, topographical, meteorological and soil factors and 9 phytochemicals of “Ningqi” No.1 fruits. There was no significant difference in carotenoids or ash in plants from the 5 regions or provinces (P ≥ 0.05), but total sugar content and total reducing sugars were lowest in Ningxia (P < 0.05), and total polysaccharides (3.61%), flavonoids (0.56%), and Se (0.62 mg/kg) were highest in Ningxia. Different chemical compounds were affected by different topographical, meteorological and soil factors. However, when taken as a whole, the most influential ecological factors were altitude, relative air humidity, accumulated temperature of ≥ 10 °C, annual mean air temperature, available potassium in soil, and annual precipitation. Except for the available potassium in soil, meteorological, and topographical factors had greatest effects on the accumulation of the main chemical compounds rather than soil factors.