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Understanding cellular metabolic systems is vital not only for determining the function of enzymatic genes, but also for elucidating the coordination among various metabolic pathways. In this context, high-throughput experiments can provide us with essential, albeit only partial information. Integration of metabolite profiling with other multiple ‘omics’ data (e.g. transcript profiling), is required to reconstruct complex networks that characterize the phenotypes in the cell. Here, we review recent approaches to integrate multiple omics data in higher plants. We especially focus on metabolomics data management, normalization, meta-omics data analysis, and an integrative approach with other omics data. Further prospects for using metabolomics and the key points to be addressed are discussed. This could be a valuable strategy for a systems-level understanding of plant systems.