A total of 539 metabolites in the flesh of 10 litchi cultivars were identified by widely targeted metabonomics based on an ultra-performance liquid chromatography-quadrupole time of flight-tandem mass spectrometry (UPLC-QTOF-MS/MS) in the multiple reaction monitoring model (MRM), and the comprehensive information about the composition and abundance of metabolites in litchi was described. Totally 298 primary metabolites (55.29%) and 228 secondary metabolites (42.30%) were found. Amino acids and their derivatives (82, 15.21%), lipids (60, 11.13%), organic acids (59, 10.95%), nucleotides and their derivatives (53, 9.83%), sugars and alcohols (25, 4.64%) were identified as the main primary metabolites, and flavonoids (129, 23.93%), phenolic acids (54, 10.02%) and alkaloids (31, 5.75%) were identified as the main secondary metabolites. Principal component analysis (PCA) and cluster heat map analysis were used to compare the metabolites of the 10 litchi cultivars. It was found that these cultivars were clearly separated into three distinct clusters according to the time of maturation and the flavor quality of the cultivars. The most important metabolies with relative content of more than 1% in each class were identified, and the contribution of each class of metabolites to the nutrition of litchi pulp was revealed. In addition, γ-aminobutyric acid, inositol, garnet acid and trigonelline were found to be abundant metabolites with unqiue functional and nutritional properties. In view of the fact that the identification of litchi metabolites can be closely related to people’s nutrition and health, as well as fruit flavor and resistance, the results of this study will provide a theoretical basis and reference information for understanding the nutrition of litchi and its cultivation, breeding, and comprehensive utilization.