Emerging evidence highlights the distribution of D-amino acids (D-AAs) in the human body and their physiological significance in human health. However, their sources from food and drug and metabolic impacts remain fully underexplored. The aim of this study was to comprehensively investigate the distribution of D-AAs in food and drug, as well as to elucidate the effects of D-AAs in feed on mouse metabolism using a mouse feeding model through non-targeted metabolic analysis. The results showed that D-AAs were detected in all the selected products, with D-aspartic acid, D-histidine, and D-leucine being the most abundant. After a 20-day feeding experiment, D-aspartic acid, D-serine, D-arginine, D-ornithine, and D-lysine were significantly accumulated in the tissues and serum of mice in a dose-dependent manner. The non-targeted metabolic analysis revealed significant differences in 11 categories of metabolites, with lipids and lipid-like molecules exhibiting the most pronounced changes. Glycerophospholipid metabolism and choline metabolism were identified as critical metabolic pathways in mice fed with D-AAs. These results suggested that D-AAs in feed may exert substantial influence on lipid metabolism and neurotransmission, immune regulation by interfering with choline metabolism and glycerophospholipid metabolism.