The basic function of carbohydrate binding module (CBM) is believed to enhance local concentration of glycosidases on the carbohydrate molecule, and thus facilitates the subsequent degradation of carbohydrate. Full understanding of the recognition mechanism of carbohydrates by CBM can be helpful to enhance the enzyme activity. In this work, the detailed recognition specificity of two soluble cello-oligosaccharide substrates, cellotetraose and cellohexaose, by a family 17 CBM from Clostridium cellulovorans was investigated by molecular dynamics simulation. Calculated binding free energies using molecular mechanics/generalized Born and surface area (MM/GBSA) approach are in excellent agreement with experimental values. Overall, based on the decomposition of total binding free energy, nonpolar terms are shown to have favorable contributions to the binding, while polar interactions make unfavorable contributions, no matter significant hydrogen bond network is formed between substrate and protein. On the basis of computational alanine scanning and per-residue free energy decomposition, Trp88 and Trp135 are shown to be two most important residues in the cellohexaose binding mainly via hydrophobic interactions. The calculated subtotal contributions for those polar residues, D54, R92, Q129, and N185, can compare very well with experimental data.