The mass spectrometry-based metabolomics approach has become a powerful tool for the quantitative analysis of small-molecule metabolites in biological samples. , an edible cyanobacterium with herbal value, serves as an unexploited bioresource for small molecules. In natural environments, undergoes repeated cycles of rehydration and dehydration, which are interrupted by either long- or short-term dormancy. In this study, we performed an untargeted metabolite profiling of samples at three physiological states: Dormant (S1), physiologically fully recovered after rehydration (S2), and physiologically partially inhibited following dehydration (S3). Significant metabolome differences were identified based on the OPLS-DA (orthogonal projections to latent structures discriminant analysis) model. In total, 183 differential metabolites (95 up-regulated; 88 down-regulated) were found during the rehydration process (S2 vs. S1), and 130 (seven up-regulated; 123 down-regulated) during the dehydration process (S3 vs. S2). Thus, it seemed that the metabolites' biosynthesis mainly took place in the rehydration process while the degradation or possible conversion occurred in the dehydration process. In addition, lipid profile differences were particularly prominent, implying profound membrane phase changes during the rehydration-dehydration cycle. In general, this study expands our understanding of the metabolite dynamics in and provides biotechnological clues for achieving the efficient production of those metabolites with medical potential.