Chlorogenic acid and its derivatives (CQAs) are considered as important bioactive secondary metabolites inGardenia jasminoidesEllis (G. jasminoides). However, few studies have investigated the biosynthesis and regulation of CQAs inG. jasminoides. In this study, methyl jasmonate (MeJA) was used to enhance CQAs accumulation in culturedG. jasminoidescells. Moreover, the possible molecular mechanism of MeJA-mediated accumulation of CQAs is also explored. To this end, time-course transcriptional profiles ofG. jasminoidescells responding to MeJA were used to investigate the mechanism from different aspects, including jasmonate (JAs) biosynthesis, signal transduction, biosynthesis of precursor, CQAs biosynthesis, transporters, and transcription factors (TFs). A total of 57,069 unigenes were assembled from the clean reads, in which 80.7% unigenes were successfully annotated. Furthermore, comparative transcriptomic results indicated that differentially expressed genes (DEGs) were mainly involved in JAs biosynthesis and signal transduction (25 DEGs), biosynthesis of precursor for CQAs (18 DEGs), CQAs biosynthesis (19 DEGs), and transporters (29 DEGs). Most of these DEGs showed continuously upregulated expressions over time, which might activate the jasmonic acid (JA) signal transduction network, boost precursor supply, and ultimately stimulate CQAs biosynthesis. Additionally, various TFs from different TF families also responded to MeJA elicitation. Interestingly, 38 DEGs from different subgroups of the MYB family might display positive or negative regulations on phenylpropanoids, especially on CQAs biosynthesis. Conclusively, our results provide insight into the possible molecular mechanism of regulation on CQAs biosynthesis, which led to a high CQAs yield in theG. jasminoidescells under MeJA treatment.