Galectins are a protein family with diverse biological functions, which are unique in specifically recognition and binding with β-galactosides as the primary structural basis for its functional performance. So far, all structurally characterized galectins display a conservative binding mode for the β-galactoside-containing carbohydrate ligands, in which one carbohydrate recognition domain (CRD) binds only one ligand. Here a novel binding pattern unique in two carbohydrate ligands for one CRD was reported, which is observed from the structure of Gal-3 CRD complexed with glycan TFN. In this doublet binding sites, Site 1 and Site 2, two TFN molecules interact with the CRD domain via two hydrogen-bond networks mediated by certain water molecules, respectively. The mutagenesis analysis shows that one of the binding sites, Site 1, is basic and essential for the carbohydrate ligands with a conservative binding mode, which should be commonly existed in galectins. While, the other binding site (Site 2) is easily discarded in a small structural interference from a single-site mutation, which illustrates that it should be conditionally appeared to play an additional and auxiliary role in ligand binding. The stereo-chemical analysis indicates that this doublet binding pattern may be suitable for some glycans with certain rather complicated constitutions, like branched structure. The possible functional role of this doublet binding pattern is also discussed.