The effects of cobalt (Co) and zinc (Zn) on the growth of Rehmannia glutinosa, as well as its antioxidant activity, total phenolic and flavonoid contents (TPC and TFC), targeted polyphenolic compounds, and molecular dynamics simulations were studied. The results revealed that exposure to 0.01 to 0.1 ppm Zn in the growth medium increased plant height, average number of leaves, and root length. Higher concentrations of Zn had deleterious effects, and lower concentrations of Co (0.01 and 0.1 ppm) significantly inhibited growth, as indicated by the retardation and reduction in root length, plant height, and leaf numbers. Higher concentrations of Co (1 ppm) cause early defoliation, necrosis, and plant death. The highest concentration of Zn (1 ppm) caused a significant decrease in Chl a concentration compared to the other concentrations and the control plants. Lower concentrations of Zn and Co (0.01 ppm) showed elevated radical-scavenging activity compared with that of the control plants. Maximum TPC and TFC were achieved at 0.01 ppm of Zn, while a higher concentration of TPC and TFC was obtained with 0.1 ppm of Co. Furthermore, catalase and ascorbate peroxidase activity were significantly affected by Zn and Co. The targeted phenolic compounds were analyzed by LC-MS-MS in the Zn- and Co-treated and control plants. Finally, to evaluate the stability of phytochemicals with high binding affinities and docking scores, a 100-ns molecular dynamic simulation was performed. These findings suggest that exposure to high concentrations of Zn- and Co-contaminated soils may affect the growth and metabolism of R. glutinosa.