Metabolomics plays significant roles in plant biology including growth, development and stress resistance. Plant produces diverse array of metabolites (approximately 200,000 to 1,000,000); hence metabolomic study is of great importance in plant biology. Due to presence of diverse array of metabolites in plants, it posses greatest challenge to indentify and quantify them correctly. Very significant improvement has been made in the field of plant metabolomics, but uniform annotation of metabolite signals in database and informatics of international standardization remains a challenge. The advancement of metabolomics largely depends upon increase in separation efficiencies and identification of individual metabolites. Fluxome and metabolomic QTL (mQTL) are very important missing link in plant metabolomics. Now these days, metabolomics is a part of system biology and metabolomics in combination with system biology approach will lead to unbiased acquisition of mass spectrometric data from diverse array of samples. To overcome different challenges, development of improved technology for detection and identification of metabolite in complex plant tissue and dissemination of metabolomic research data will be very helpful.