Metabolic engineering is a powerful approach for optimization of fermentation processes for more efficient production of desired products. Metabolic engineering can be categorized three parts: genetic modification, analysis and design. Analytical techniques such as expression analysis, protein analysis and metabolic pathway analysis enabled more rational design for strain improvement and biomolecules production. Metabolic flux analysis, which allows calculation of the intracellular metabolic fluxes based on the stoichiometry of intracellular reactions and mass balances around the intracellular metabolites, has become an essential tool for metabolic engineering. In this study, metabolic flux analyses were carried out to optimize metabolic pathways for maximum production of desired products. The optimized metabolic pathways for production of 6 metabolites (acetic acid, lactic acid, malic acid, pyruvic acid, succinic acid, ethanol) and 3 amino acids (aspartic acid, phenylalanine, glutamic acid) were predicted by metabolic flux analyses. Based on optimized metabolic pathways, new efficient metabolite production systems could be suggested, and enhanced production of metabolites might be achieved.