Abstract: Metabonomics is attracting more and more attention in different fields of life science including disease study and drug discovery and development. It is very important to collect the data of as many metabolites as possible in a faster way, especially in a run. Unfortunately, comprehensive analysis of metabonome and the unequivocal identification of the detected metabolite candidates are still a bottleneck of current metabonomics studies. For these challenges our group developed a multi-dimensional chromatography consisting of a HILIC column and a RP-HPLC column to increase the peak capacity. In the meantime, an integrated identification method was established based on LC/MSn, multivariate statistic analysis, FT-MS, database search, GC retention index and so on.