To explore the differences of metabolites in the mature fruits of yellow raspberry and red raspberry， nontargeted LC-MS metabolomics analysis was carried out. A total of 708 (98 known) significantly differentially expressed metabolites were detected in the positive ion mode. In the negative ion mode， there were 780(45 known) significantly differentially expressed metabolites. Through the metabolic enrichment analysis of KEGG database， 1 566 differentially expressed metabolites in red raspberry and yellow raspberry fruits are enriched in four categories: metabolism， genetic information processing， environmental information processing and human diseases. These differentially expressed metabolites were enriched in 66 pathways， and the metabolic pathways (ko01100) enriched the most differential metabolites (34 species). In addition， delphinidin 3-glucoside， (s)-abscisic acid， hydrocinnamic acid and hesperetin in yellow raspberry fruits were -1.496， -1.632， -1.527 and -0.477-fold lower than those in red raspberry fruits， respectively. Protochlorophyllide was up-regulated more than 10 times in yellow raspberry fruit. The results provide theoretical basis for the development and utilization of specific compounds in different raspberry fruits.