The invention relates to a multi-dimensional ion chromatographic analysis system, belonging to the chemical field of analysis. To solve the problem that a conventional chromatographic technique is insufficient in separation of molecules such as various organic acid, amino acid, sugar and alcohol in complex samples, a set of multi-dimensional ion chromatographic analysis system is developed; the system comprises a plurality of pumps, one or more changeover valves and a plurality of detectors; by utilizing the difference of separation mechanisms of target components on chromatographic columns and the difference of retention time of the components, and through a plurality of chromatographic switchover enrichments and valve switchover time selection, ion chromatographic connected systems of two-dimension, three-dimension, four-dimension, five-dimension and higher can be established according to difference of target components to be separated, so that the coseparation analysis of water-soluble metabolite such as organic acid, amino acid, sugar and alcohol of complex samples is realized. By utilizing the multi-dimensional ion chromatographic analysis system, the complex sample can be rapidly, sufficiently and precisely separated and identified, and the mutual interference among the components is eliminated.