Abstract: To explore the changes of gene expression in Phyllanthus Emblica fruits and the possible mechanism of medical traits formation, transcriptomes of 4 Phyllanthus Emblica germplasms were sequenced by Hiseq2500PE125, based on the basic bioinformatics analysis and expression profile gene annotation, the relative functional genes of medical traits in Phyllanthus Emblica fruits were predicted. The results showedthat Phyllanthus Emblica fruits had 192375 transcripts, 47573 unigenes, and the average transcript length was 1140 bp. The functional gene predictions showed that the ways on carbon metabolism had the highest proportion in fruits, up to 44.2%, and amino acid metabolism pathways were 441, which revealed that the carbon metabolism and amino acid metabolism activity were strong in the forming process of fruit medicinal properties. Due to the consensus that the medicinal components of Phyllanthus Emblica germplasms are phenolic acid compounds, the conclusion provides references for the further studies on the functional genes and regulation of the secondary metabolites in Phyllanthus Emblica.