Metabolomics is an omics technology that studies the types, quantities, and changes of endogenous metabolic substances in organisms affected by abiotic and biotic factors. Background/Objectives: Based on metabolomics, small molecule metabolites in biological organisms can be qualitatively and quantitatively analysed. This method analysis directly correlates with biological phenotypes, facilitating the interpretation of life conditions. Wheat (Triticum aestivum L.) is one of the major food crops in the world, and its quality and yield play important roles in safeguarding food security. Methods: This review elaborated on the significance of metabolomics research techniques and methods in enhancing wheat resilience against biotic and abiotic stresses. Results: Metabolomics plays an important role in identifying the metabolites in wheat that respond to diverse stresses. The integrated examination of metabolomics with other omics disciplines provides new insights and approaches for exploring resistance genes, understanding the genetic basis of wheat metabolism, and revealing the mechanisms involved in stress responses. Conclusions: Emerging metabolomics research techniques to propose innovative avenues of research is important to enhance wheat resistance.