To demonstrate the fructose metabolism pathway in Bifidobacterium Longum NCC2705 and to construct its fermentation model, we explored the comparative proteome cultivating the strain on glucose or fructose, based on a proteomic reference map of B. longum NCC2705 constructed earlier. Then, we used matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) mass spectrometry and electro-spray ionization tandem mass spectrometry (ESI-MS/MS) for differently expressed proteins identification. Furthermore, with semi-quantitative RT-PCR we determined the distinctively expressed proteins at the level of transcription. Proteomic comparison of glucose- and fructose-grown cells demonstrated much similarity. On the page of fructose there were all the enzymes and proteins that exist during the process of glucose degradation. We observed a greater variation of more than three-fold for the identified 9 spots representing 5 protein entries by MALDI-TOF MS. The sugar-binding protein specific to fructose (BL0033) and an ABC transporter ATP binding protein (BL0034) showed higher expression level from cells grown on fructose. It was also determined by semi-quantitative RT-PCR subsequently. BL0033 time course and concentration experiments showed that the induction time correlated to higher fructose concentration, and increased expression of BL0033. Fructose was catabolized via the same degradation pathway as glucose at the level of proteomics. BL0033 was induced by fructose. All results suggest that the uptake of fructose into the cell may be conducted by a specific ABC transport system, in which BL0033 and BL0034 as components might have played an important role.