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<i>Salvia miltiorrhiza</i> Bunge has been widely used in the treatment of cardiovascular and cerebrovascular diseases, due to the pharmacological action of its active components such as the tanshinones. Plasma membrane (PM) H⁺-ATPase plays key roles in numerous physiological processes in plants. However, little is known about the PM H⁺-ATPase gene family in <i>S. miltiorrhiza</i> (<i>Sm</i>). Here, nine PM H⁺-ATPase isoforms were identified and named <i>SmPHA1–SmPHA9</i>. Phylogenetic tree analysis showed that the genetic distance of <i>SmPHAs</i> was relatively far in the <i>S. miltiorrhiza</i> PM H⁺-ATPase family. Moreover, the transmembrane structures were rich in <i>SmPHA</i> protein. In addition, <i>SmPHA4</i> was found to be highly expressed in roots and flowers. HPLC revealed that accumulation of dihydrotanshinone (DT), cryptotanshinone (CT), and tanshinone I (TI) was significantly reduced in the <i>SmPHA4-OE</i> lines but was increased in the <i>SmPHA4-RNAi</i> lines, ranging from 2.54 to 3.52, 3.77 to 6.33, and 0.35 to 0.74 mg/g, respectively, suggesting that <i>SmPHA4</i> is a candidate regulator of tanshinone metabolites. Moreover, qRT-PCR confirmed that the expression of tanshinone biosynthetic-related key enzymes was also upregulated in the <i>SmPHA4-RNAi</i> lines. In summary, this study highlighted PM H⁺-ATPase function and provided new insights into regulatory candidate genes for modulating secondary metabolism biosynthesis in <i>S. miltiorrhiza</i>.