The major player for catabolite repression is the phosphotransferase systems (PTSs) and cAMP-Crp. Moreover, Cra controls the carbon flow in the metabolic network. In the present research, the effect of modulating cra gene (Δcra) on the consumption of multiple carbon sources such as glucose and fructose (as well as xylose) was investigated under both aerobic and anaerobic conditions. It was shown that glucose and fructose could be co-metabolized with fructose consumed faster than glucose in cra mutant under both aerobic and anaerobic conditions. It was also implied that cra mutant consumed higher amount of total carbon sources, which contributed to the highest metabolite production as compared to the wild type strain. Thus, cra mutant can be a good candidate for the efficient utilization of multiple carbon sources such as glucose and fructose, where xylose consumption was repressed by catabolite repression. The overall regulation mechanisms were clarified based on fermentation data and gene transcript analysis.