This research compared the transcriptomes of four different tissues of Pinus koraiensis by using RNA-seq technique and a lot of differentially expressed unigenes were obtained. A total of 21.3 GB of data was obtained and 41 476 expressed unigenes were received after assembling. Through GO and COG classification, the commented and transcribed sequences were classified into 24 or 56 functional categories, which referred to many biochemical processes such as material and energy metabolism, signal transduction, transcriptional regulation and defense reaction. Through pathway enrichment analysis, the pathways associated with grease synthetic fatty acid biosynthetic and terpenoids synthesis were found. Two unigenes of metabolic pathways in KEGG database were compared and 16 key enzyme genes of fatty acid synthesis in other species homologous and 34 key enzyme genes of terpenoid biosynthetic pathway were obtained. By high-throughput sequencing and bioinformatics research, a large number of Pinus koraiensis transcriptome unigenes was obtained. This research provides references for the research on the genes related to secondary metabolites synthesis in Pinus koraiensis.