Korla fragrant pear (KFP) with special fragrance is a unique cultivar in Xinjiang, China. In order to explore the biosynthesis molecular mechanism of chlorogenic acid (CGA) in KFP, the samples at different development periods were collected for transcriptome analysis. High performance liquid chromatography analysis showed that CGA contents of KFP at 88, 118 and 163 days after full bloom were (20.96 ± 1.84), (12.01 ± 0.91) and (7.16 ± 0.41) mg/100 g, respectively, and decreased with the fruit development. Pears from these typical 3 periods were selected for de novo transcriptome assemble and 68059 unigenes were assembled from 444037960 clean reads. One ‘phenylpropanoid biosynthesis’ pathway including 57 unigenes, 11 PALs, 1 PTAL, 6 4CLs, 9 C4Hs, 25 HCTs and 5 C3'Hs related to CGA biosynthesis was determined. It was found that the expression levels of 11 differentially expressed genes including 1 PAL, 2 C4Hs, 3 4CLs and 5 HCTs were consistent with the change of CGA content. Quantitative polymerase chain reaction analysis further showed that 8 unigenes involved in CGA biosynthesis were consistent with the RNA-seq data. These findings will provide a comprehensive understanding and valuable information on the genetic engineering and molecular breeding in KFP.