Abstract: To analyze the flavonoid biosynthesis pathway in Clinopodium chinense (Benth.) O. Kuntze and to explore the role of microRNAs (miRNAs) in target gene regulation, transcriptome sequencing of small RNAs (sRNAs) in the roots, stems, and leaves of C. chinense was carried out using the BGISEQ-500 platform. In total, 86 conserved miRNAs were identified, divided into 26 families, and eight novel miRNAs were predicted. Three candidate miRNAs (novel_mir3, miR167d-5p, and miR396h) and their target genes involved in the flavonoid biosynthesis pathway were screened out. Sequence analysis and homologous modeling of 4-coumarate-CoA ligase, a key enzyme encoded by a target gene, showed that it had two conserved peptide motifs and a highly conserved substrate binding groove and catalytic domain. This research lays a foundation for functional genomics study of C. chinense and understanding the regulation mechanism of flavonoid biosynthesis.