Plant growth and yield are affected often by stress conditions including drought, which is the most important abiotic stress to reduce crop production worldwide. Milk thistle is one of the momentous medicinal crops with high potential as a multiple-purpose plant for low-efficient cultivation systems in the arid and semiarid areas. In this experiment, the effect of Chitosan (100 and 200 mg/l) and salicylic acid (0.5 and 1 mM) was investigated on plant traits (morphological, physiological, and phytochemical) under different levels of water deficit (Field capacity (F.C), 70% F.C, 40% F.C). Data were recorded in a time course (3, 7, 14, and 21 days after stress) and subjected to statistical analyses. According to the results, morphological, physiological, and phytochemical traits of the plant were significantly affected by water deficit, elicitors, and stress durations. Comparing the stress levels showed that severe water stress (40% F.C) significantly reduced growth and yield, while mild stress (70% F.C) did not show significant difference to non-stress treatment (F.C). The results showed that both chitosan and salicylic acid elicitors increased growth and yield, stress tolerance of plants under water-deficit conditions, and promotion of flavonoids, but chitosan has a more prominent effect. Under severe stress conditions, chitosan increased the yield of fresh and dry weight by 76.4% and 72.4%, but salicylic acid increased fresh weight and dry weight by 27.1% and 58.8%, respectively. Conversely, salicylic acid resulted in a 77.8% increase in grain yield, while that of chitosan was 75.0%. On the other hand, the content of silybin A in treatments of salicylic acid and chitosan, was increased by 2.9 and 9.2 mg/g, respectively, while the content of silybin B was increased by 6.48 and 9.48 mg/g, respectively. The role of the elicitors in reducing the negative effects of water stress and plant tolerance is due to stimulation of osmoregulation through proline and soluble sugar accumulation, reduction of malondialdehyde level, and production of antioxidant enzymes.