Prediction and analysis of molecular structure and biochemical function are of theoretical guiding significance for gene discovery and application, and considered as one of the central problem of computational biology. Here, some characteristic features of chalcone synthase (CHS) family from Scutellaria baicalensis were described via bioinformatic analysis, and showed as following: the nucleic acid sequences and amino acid sequences of three chs member genes shared high similarity in the molecular structures and physicochemical properties; SbCHS proteins were localized to the cytosol, and possessed a good hydrophobic nature, with lacking any transmembrane topological structure. The phylogram analysis suggested that they were a group genes with significant functional association and genetic conservation. The secondary structures of the SbCHSs were mainly composed of α-helixes and random coils, and the tertiary structures contained malonyl CoA linkers, besides, each of CHS-A and CHS-B with N-glycosylation motif included. Taken together, these results demonstrate that CHS family from S. baicalensis has the typical molecular structure and function of chalcone synthase, compared with the experimental data for Medicago sativa CHS protein.