In environments with limited winter food resources and high latitudes, large wild ungulates must balance toxic and harmful secondary metabolites in plants, avoid harmful substances, and choose beneficial components to form a specific food composition pattern. As the subject of this study, red deer (Cervus elaphus xanthopygus) was was chosen. In this study, we collected fecal samples from wild red deer and their foraged plants by backtracking footprint chain and non-invasive sampling methods in the territory of Heilongjiang Muling Japanese Yew National Nature Reserve in November 2020. The winter food composition of red deer in the protected area was determined by fecal micro histological analysis, and the winter food composition pattern of red deer was uncovered through k-means cluster analysis. Contents of secondary metabolites of some plant species were detected qualitatively and quantitatively using a widely targeted metabolome technology, and statistical analysis was performed to investigate the effects of plant secondary metabolites on the food composition pattern of red deer population. Through the analysis of fecal residue, it was determined that the red deer population in the reserve fed on 30 plant species during the winter, among which woody plants accounted for 92.48%. Three different food composition patterns dominant by Taxus Cuspidata, Acer Barbinerve and Corylus mandshurica as the main food found. A total of 638 secondary metabolites were detected using widely targeted metabolome technology with broad targeting. 25 of them were significantly correlated with red deer feeding frequency. Most of terpenoids inhibited feeding of red deer, whereas tannins had a certain positive effect on feeding selection of red deer. The results of Mantel test revealed that the relative contents of some flavonoids, tannins and terpenoids in the 25 substances above were significantly correlated with the individual food composition of different red deer, to illustrate these metabolites relative content and nature of the differences will lead to different populations in different individual differences in food composition, population is in one of the reasons to form different patterns of the food composition. The flavonoids mainly affected the red deer population feeding on Taxus Cuspidata, while the tannins and terpenoids mainly affected the red deer population feeding on Corylus mandshurica and Acer Barbinerve. This study reveals the possible factors for the differences in winter food composition patterns of red deer populations in this region from the perspective of plant secondary metabolites, and provides a foundation for further research on the relationship between trophic strategies and chemical defense of large ungulates.