Algae have been investigated and developed as a source of food, dietary supplement, and biofuel, due to their chemical and nutrient composition. Algae consumption carries algal proteins, polyunsaturated fatty acids (PUFAs), vitamins, dietary fibers, and bioactive compounds into the biological systems of humans and animals, and therefore are expected to elicit metabolic and physiological responses. Numerous efforts have been undertaken to understand the health-promoting effects of algae consumption, such as their hypolipidemic, antioxidant, anti-obesity and anti-cancer properties. 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. The growth performance was significantly increased by 5% algae but decreased by 20% algae feeding. 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 revealed diverse influences of algae feeding on mouse metabolome, which are represented by the features as follows: 1). Urinary vitamins and fecal pigments are identified as robust exposure markers of algae feeding. 2). Despite the high-level protein in algae, the impacts of algae feeding on free amino acids in serum and the liver were quite limited. 3). Algae feeding increased the PUFA levels in serum and liver lipidomes and the free fatty acids in feces. 4). 5% algae increased the level of reduced glutathione (GSH) in the liver while 20% algae increased the level of oxidized glutathione (GSSG) in the liver and the levels of aldehydic lipid oxidation products (LOPs) in the liver and urine. 5). 5% algae selective increased the levels of intermediate metabolites, including adenosine monophosphate (AMP), adenylsuccinic acid, dephospho-CoA, and nicotinamide, in the liver while 20% algae increased the levels of carnitine and carnitine derivatives in the liver. 6). Algae feeding dramatically altered the microbial metabolism, as reflected by the increases in short-chain fatty acids (SCFAs) and primary bile salts in feces, the increases of branched fatty acids in urine, the decreases of secondary bile acids in feces, and the decrease of p-cresol metabolites in 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.