Scenedesmus is a common green algae genus with high biomass productivity, and has been widely used in biofuel production and waste water management. However, the suitability and metabolic consequences of using Scenedesmus as an animal feed ingredient have not been examined in detail. In this study, the influences of consuming Scenedesmus on the metabolic status of young mice were investigated through growth performance, blood chemistry, and liquid chromatography-mass spectrometry (LC-MS)-based metabolomics. Compared to the control diet, feeding a diet containing 5% Scenedesmus improved growth performance while the diet containing 20% Scenedesmus suppressed it. Among common macronutrients-derived blood biochemicals, serum triacylglycerols and cholesterol levels were dramatically decreased by feeding the 20% Scenedesmus diet. Metabolomic analysis of liver, serum, feces, and urine samples indicated that Scenedesmus feeding greatly affected the metabolites associated with amino acid, lipid, purine, microbial metabolism, and the endogenous antioxidant system. The growth promotion effect of feeding the 5% Scenedesmus diet was associated with elevated concentrations of antioxidants, an expanded purine nucleotide cycle, and modified microbial metabolism, while the growth suppression effect of feeding the 20% Scenedesmus diet was correlated to oxidative stress, disrupted urea cycle, upregulated fatty acid oxidation, and an imbalanced lipidome. These correlations among Scenedesmus dietary inclusion rate, individual metabolite markers, and growth performance suggest the need to define the dietary inclusion rate threshold for using Scenedesmus and other microalgae supplements as feed ingredients, and also warrant further mechanistic investigations on the biological processes connecting specific constituents of Scenedesmus with the metabolic effects observed in this study.