Objective In order to clarify the structural gene information of Sophora flavescens chalcone isomerase (sfCHI) and its expression pattern among distinct organs. Methods This experiment took advantage of S. flavescens deep transcriptomic data to clone sfCHI gene and conducted bioinformatics analysis on the cDNA sequence. Semi-quantitative PCR was used to detect the expression of sfCHI gene in different organs of S. flavescens. Results The results showed that the cDNA sequence of S. flavescens CHI gene was 1 265 bp in length and contained a 630 bp open reading frame (ORF) encoding 209 amino acids. Sequence analysis showed that the similarity between sfCHI and Lupinus angustifolius CHI gene was the highest, up to 89.95%. Phylogenetic tree resulted from 16 selected CHI genes showed that sfCHI and other related genes from Leguminosae were in the same group. Semi-quantitative PCR results showed that sfCHI gene expression in the root of S. flavescens is the lowest, while expression in leaves, petioles and stems did not show obvious difference. Conclusion In this study, the sequence information and physicochemical characteristics of the gene were firstly clarified by gene cloning of the chalcone isomerase gene and the expression analysis of different tissues, which will promote the study of biosynthetic mechanism of flavonoids in S. flavescens.