Abstract: Metabolomics, as a high-throughput research method, has wider application in horticultural crops. However, there were still little reports covering the research and development of the technology. As a reference article for gardeners, this paper summarized the application of metabolomics both at home and aboard. It presented the achievements of the metabolic network analysis and control, genetic function identification, evaluation of the safety of transgenic technology, resistance identification, quality formation, evaluation of horticultural techniques，postharvest treatment, identification of quality and origin, etc. It also pointed out the existed problems and proposed the research directions. The paper believed that metabolomics was a valuable supplement to traditional horticultural crops research and the integration of metabolomics, transcriptomics, proteomics and genomics would be the developing direction of horticultural crops metabolomics.