Siraitia grosvenorii is an economic and medicinal plant, its fruit is considered to be good to health for its diverse bioactive ingredients. However, the clarification of chemical composition and their changes after saccharification procedure are not well performed. In present study, a metabolomics method based on ultra-high-performance liquid chromatography tandem quadrupole time-of-flight mass spectrometry was developed for metabolic profiling acquisition of Siraitia grosvenorii extract. Furthermore, information dependent analysis (IDA) combined with self-constructed LC–MS/MS identification system for metabolites were employed to identify primary and secondary metabolites in Siraitia grosvenorii. A total of 126 metabolites were identified or tentatively identified. The obvious differences of metabolic profiling between green fruit and saccharified yellow fruit were observed, and metabolites showed their own distribution characteristics in peel, flesh and seed. The majority of the nutrients and effective components were more distributed in flesh and peel, and saccharification was conducive to accumulation of sweet glycosides. This study not only expanded metabolite composition information of Siraitia grosvenorii, but also specified distribution characteristics of identified metabolites.