Metabolomics is the qualitative and quantitative study of the whole metabolome within a biological system. Metabolomics attempts to systematically integrate metabolic processes using data accumulated from nuclear magnetic resonance (NMR) and mass spectrometry (MS). NMR exploits the absorption and re-emission of electromagnetic radiation by nuclei exposed to a magnetic field. Additionally, NMR reveals the specific quantum mechanical magnetic properties of the atomic nucleus. MS is an analytical technique that provides spectra of the masses of the atoms or molecules comprising a sample. From these spectra, researchers can determine the elemental or isotopic signature of a sample, the masses of its constituent particles and molecules, and the chemical structures of molecules such as peptides. NMR and MS are among the most widely used technical platforms in metabolomics research, enabling the acquisition of detailed and systematic information of the biological systems under study. Currently, metabolomics has become an effective tool in researching traditional ecologies such as soil and marine ecology. At present, metabolomics is increasingly connecting with other systematic 'omics' fields such as proteomics and genomics. The fusion of ecology with metabolomics and the merging of metabolomics with other relevant techniques promise the establishment and development of a new 'omics' field-ecological metabolomics, or ecometabolomics. Ecometabolomics primarily aims to identify the global metabolomic response of an organism to environmental changes, and thereby enhance our understanding of how different species interact and co-evolve. Increasingly, ecologists are recognizing the importance of understanding how the metabolome and total number of metabolites respond to environmental changes. In four sections, this paper discusses recent applications of metabolomics techniques in ecological studies. The first section introduces the concepts of metabolomics and ecometabolomics and outlines their developmental history. The second section focuses on the widely used NMR and MS techniques. NMR includes ¹H NMR, ¹³C NMR, ³¹P NMR, ¹⁷O NMR and ¹⁵N NMR, whereas MS techniques include gas chromatogram-mass spectrometry (GC-MS), liquid chromatogram-mass spectrometry (LC-MS), and directed infusion or injection mass spectrometry (DIMS). In the third section, the application status of metabolomics techniques in ecological research is discussed from two perspectives. At the biological tissue level, metabolomics has been applied to individual, population, and community ecologies. At the organism level, it has been adopted for species-level identification in animal ecology, plant ecology and microbial ecology. The forth section discusses the future challenges and perspectives of ecometabolomics. First, metabolomics will become more comprehensively integrated with other systematic biological techniques. Second, multiple analytical methods and techniques adopted in metabolomics will be simultaneously applied to single biological samples, enabling the synchronous accumulation of qualitative and quantitative data within a very short time. Third, a metabolomics database will be compiled and expanded to facilitate scientific research and to increase the analytical efficiency of both bioinformatics and metabolomics. The paper also suggests the roles for future ecologists. In conclusion, techniques relevant to metabolomics will be widely and intensively applied in ecological research such as pressure response, life cycle variation, population structure, interaction and circulation of nutrients, and ecological niches.