Drought is a significant abiotic constraint in Salvia miltiorrhiza production, particularly during seedling cultivation. Therefore, researching drought resistance is crucial. This study aimed to investigate the effects of drought stress on the agronomic and physiological characteristics of S. miltiorrhiza at the seedling stage, evaluate drought resistance of various germplasms, and identify drought resistance markers. To simulate drought stress, five different concentrations of polyethylene glycol (PEG) (0%, 5%, 10%, 15%, and 20%) were applied to four S. miltiorrhiza germplasms at the seedling stage. Agronomic traits, root morphology, and physiological and biochemical indicators were measured. The data were then analyzed using the membership function method, correlation analysis, and stepwise regression analysis. The results revealed that as the PEG concentration increased, the aboveground agronomic traits and underground root morphology of the four S. miltiorrhiza germplasms showed a decline. The activities of catalase and peroxidase initially increased and then decreased, while the contents of soluble sugar (SS), soluble protein, and proline increased compared to the control. Based on the membership function values of 16 morphological and physiological indicators, the drought resistance order of the four S. miltiorrhiza germplasms was as follows: Yudanshen VD > Yudanshen VA > Yudanshen VB > Yudanshen VC. Additionally, an optimal regression equation (D = 0.887X1 -0.003X2 + 0.142X3) was developed through stepwise regression analysis, indicating that X1, X2, and X3 represent the maximum root length, root surface area, and SS content, respectively. Consequently, this study presents a comprehensive and reliable method for evaluating drought resistance in S. miltiorrhiza germplasm resources.