Abstract:Metabolomics has become one of the most important areas in systems biology, to qualitatively and quantitatively analyze all endogenous metabolites and reveal the relationship between physiological/pathological changes or environmental perturbation and biological metabolism. Metabolomics has the characteristics of high sensitivity, wide selection range and fast analysis speed, and so it plays an increasing role in the microalgae studies. In this review, we summarize the research process, analysis methods, development trends and challenges of metabolomics in microalgae researches, to provide new ideas and strategies for bioenergy utilization, environmental protection, and high-value bioproducts of microalgae.