Abstract: Metabolic engineering is the improvement of cellular properties by using modern genetic engineering tools.Metabolic engineering encompasses three important steps：the modification of cellular pathways（synthesis），the rigorous evaluation of the phenotype of the modified cells（phenotype characterization）and optimization design of further genetic modification（design）.In the procedure，“Omics”（genomics，transcriptomics，proteomics，metabolomics，fluxomics）analyses play a very important role in the phenotype characterization.Because the environmental conditions have also great effects on the cellular properties，so the changes of the cellular properties under different environmental conditions must be evaluated by the “Omics” analyses.Based on the “Omics” analyses，it is possible to get valuable knowledge that can be used for the development of metabolic engineering strategies，which consequently are used to optimize the bioprocess.In this paper，the recent advances of metabolic engineering combined with functional genomics are reviewed.