Salvia miltiorrhiza, known as danshen, is one of most valued medicinal plants in China. Although it has been cultivated since ancient times, an optimal culture system needs to be standardized for this important species. Here, we explored the phytochemical properties of S. miltiorrhiza with the treatments of rare earth elements (REEs) to develop an optimal tissue culture system. Four-week-old in vitro-grown S. miltiorrhiza plantlets were used as explants. The experiment was conducted in a randomized block design on a Murashige and Skoog (MS) medium containing 0.2 mg·L−1 naphthaleneacetic acid (NAA) to induce rooting at four different concentrations (50, 100, 200, and 300 μM) of REEs such as cerium (Ce), lanthanum (La), or praseodymium (Pr), respectively. Compared with all REEs at different concentrations, 100 μM Pr induced greater root length than Ce or La at any concentrations. Concomitantly, 0.38 μg tanshinone IIA/mg dry weight (DW) was observed, which was 54.84% higher than in the control. Similarly, chlorophyll content, antioxidant enzyme activity, and secondary metabolite were enhanced in rooting medium supplemented with 100 μM Pr. Therefore, this study showed that 100 μM Pr is an adequate concentration in the optimal culture system for promoting plant growth as well as enhancing secondary metabolite content in S. miltiorrhiza.