The fruit of Schisandra chinensis Turcz. (Baill.), namely "Wuweizi" in China, is a well-known herbal medicine and health food. At present, research focused on the extraction of effective chemical component and function identification. Little known about the secondary metabolism gene pathway of chemical composition. Its fruit color usually red, however, the white fruit color variation has been found. It made us interested in exploring which gene change lead to this result. In order to understand the genetic background of S. chinensis, we performed a transcriptome analysis of S. chinensis, including red fruit and skin of 'Yanhong' cultivar and white fruit and skin of 'Jinwuwei'. We obtained 26.4 GB raw data (NCBI accession number: SSR4449123). De novo transcriptome assembly using Trinity revealed 92,415 transcripts and generated 71,443 unigenes. All unigenes were annotated in database. This study provides transcriptome of S. chinensis, which might be useful for comparative transcriptome analyses and understand gene expression of secondary metabolites.