Elementary flux mode (EFM) analysis was used in the metabolic analysis of central carbon metabolism in Saccharomyces cerevisiae based on constructed cellular network. Calculated from the metabolic model, the ethanol-producing pathway No. 37 furthest converts the substrate into ethanol among the 78 elementary flux modes. The in silico metabolic phenotypes predicted based on this analysis fit well with the fermentation performance of the engineered strains, KAM3 and KAM11, which confirmed that EFM analysis is valid to direct the construction of Saccharomyces cerevisiae engineered strains, to increase the ethanol yield.