Metabolomics uses advanced analytical chemistry techniques to comprehensively identify, quantify, and characterize a large number of small molecule metabolites in biological samples (e.g., milk, plasma, and serum). It is routinely used in biomedical, nutritional, crop and farm animal research. Metabolomic analyses in farm animals have been initiated in many non-genetic application fields. Recently, it is being increasingly used in animal breeding with the emergence of physiological genomics/genetics and refined phenotypic description. In this review, we describe the features of metabolomics platforms and approaches, and summarize the metabolomics applications in animal genetics and genomics with a focus on some key areas, such as the heritability estimates of metabolomic profiles, identification differences metabolites between lines or breeds, genome-wide association studies with metabotypes, biomarker discovery for economic traits. Moreover, we also discuss the potential applications based on current livestock metabolomics studies. The intent of this review is to provide a critical overview of the trends in the applications of metabolomics in animal breeding, aiming to provide a reference for further studies on the genetic background of the important traits of farm animals combined metabolomics with genomics.