Plant cell culture technology is a promising alternative for production of high-value secondary metabolites,but limited by production decline after long term sub-culture,and the entire mechanisms were still unclear.The goal of this study was to gain insights into production decline at both mRNA and miRNA levels by high-throughput sequencing,using two typical Taxus cell lines,CA(sub-cultured for 10 years)and NA(sub-cultured for 6 months).Obviously,CA decreased most genes involved in secondary metabolites biosynthesis,and increased those genes related to primary metabolism such as oxidative phosphorylation,nucleotide/protein anabolism and metabolism.Interestingly,CA preferred MEV pathway while NA preferred MEP pathway in terpenoid backbone biosynthesis,less efficiency pathway caused a decreasing production of terpenoids,which indicated that the production decline was a network conversion.Then,the miRNA regulation systems of the conversion were analyzed according to our integrated data.miRNA regulated many functional-enzyme and transcriptional factor(TF)genes involved in primary-and secondary-metabolism pathway.miRNA-TF-genes was a regulation system for the production decline.And miR8154 and miR5298b targeted a mass of differentially expressed(DE)genes including TF,methyltransferases and functional enzyme genes.However,most key genes were not targeted by DE miRNA but their potential TF were significantly differentially expressed,and expression of several nucleotide/histone-methyltranferase genes were increased in CA.That inferred that TF and methylation,the complementary regulation system of miRNA,were seemed to involve in the production decline.Our current studies could be helpful to guide the industrial usage of long term sub-culture cells.