Goji (Lycium barbarum L.) is a highly medicinal value tree species. The yield and nutritional contents of goji fruit are significant affected by fertilizer level. In this study, we analyzed the yield and nutritional contents change of goji fruit, which planted in pot (vermiculite:perlite, 1:2, v:v) in growth chamber under P0 (32.5 g/per tree), P1 (65 g/per tree), and P2 (97.5 g/per tree). Meanwhile, we utilized an integrated Ultra Performance Liquid Chromatography-Electrospray Ionization-Tandem Mass Spectrometry (UPLC-ESI-MS/MS) to analysis of the response of the metabolome in goji fruit to phosphorus level. The results show that the yield of goji fruits had strongly negative correlation with phosphorus level, especially in the third harvest time. The amino acids, flavonoids, polysaccharides, and betaine contents of goji fruits in the first harvest time had obvious correlated with the level of phosphorus level. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment results indicated that the impact of different phosphorus fertilizer levels on each group mainly involved the biosynthesis of flavonoids. The results provide new insights into the theoretical basis of the relationship between the nutritional contents of goji fruits and phosphorus fertilizer level. Lycium barbarum L., well known as goji or wolfberry, is an economic tree species belonging to the Solanaceae family. It is widely distributed in the arid and semi-arid areas of northwestern China, Southeastern Europe, and the Mediterranean areas 1,2. In China, there are seven species and three varieties that are mainly cultivated in the northwest and northern parts of the country 3. Because its fruit is rich in nutrients, such as amino acids, polysaccharides, and flavonoids etc., the goji fruit is also called a "super fruits", and has become popular around the world, with a rapid sequence of new products entering a dynamic and further growing market 4. Phosphorus plays an important role in the growth and metabolism of plants and is also an important component of the plant protoplasm as well as nucleic acids and nuclear proteins 5,6. As a structural element and regulatory factor in plants, phosphorus is involved in the metabolic pathways of the three major metabolites of plants, and as an enzymatic reaction substrate, it is involved in the reaction process of photosynthesis and respiration as well as in the regulation of enzyme activity, ensuring the normal growth and development of plants. Phosphorus is also an important role in the inner energy transfer of plant, such as phosphate esters. Most of phosphate esters are intermediates of biosynthesis and metabolic degradation. Their function and formation are directly related to energy metabolism and energy-rich phosphate. For example, the energy required for starch biosynthesis or ion absorption is composed of an energy-rich intermediate or coenzyme (mainly ATP). When Energy liberated during glycolysis, respiration, or photosynthesis is utilized for the synthesis of the energy-rich pyrophosphate bond, an...