Algae have been investigated and developed as a source of food, dietary supplement, and biofuel, due to their chemical and nutrient composition. However, the metabolic events in algae-elicited effects were not examined in details in spite of the fact that these benefits are largely based on the metabolic interactions between algal components and the biological system.  In this study, the influences of consuming green algae (Scenedesmus sp.) on the metabolic status of young mice was investigated through growth performance, blood chemistry, and liquid chromatography-mass spectrometry (LC-MS)-based metabolomics. Compared to the control diet, 5% algae promoted growth performance while 20% algae suppressed it. Serum glucose, triacylglycerols (TAG), and blood urea nitrogen (BUN) levels were not affected by both treatments, but serum cholesterol level was dramatically decreased by 20% algae feeding. Metabolomic analysis of liver, serum, feces and urine samples indicated that algae feeding greatly affected the metabolites belonging to amino acid, lipid, microbial metabolism and antioxidant system. The growth promotion effect of 5% algae feeding was associated with the increased levels of hepatic reduced glutathione, niacinamide, dephophocoenzyme A, and adenylsuccinic acid. In contrast, the growth suppression effects of 20% algae feeding was correlated to the increased level of oxidized glutathione and carnitine in the liver, increased EPA and DHA in liver and serum, and increased acyl-glycine in the urine. Overall, multiple correlations between metabolite markers and growth performance in algae feeding were established in this study and could serve as a foundation for further mechanistic investigations on the biological effects of algae feeding.