Salicylic acid (SA) mediates tolerance mechanisms in plants against a wide spectrum of biotic and abiotic stresses. Therefore, the present study was carried out to determine how SA regulates the plant protection mechanisms in two cultivars of oilseed rape (Brassica napus L.) under chromium (Cr) stress. Exogenously applied SA enhanced plant growth, increased dry biomasses, and strengthened the reactive oxygen scavenging system by improving cell organelles that were severely damaged via Cr toxicity. The contents of Cr were significantly enhanced in both root and leaf of cultivar Zheda 622 (yellow color) compared with cultivar ZS 758 (black color). Exogenous application of SA significantly reduced the Cr contents in both plant organs as well as enhanced the SA contents under Cr stress. A dose-dependent increase was observed in reactive oxygen species (ROS) generation under Cr stress. To ease the inimical effects of ROS, plants' defense systems were induced under Cr stress, and SA further enhanced protection. Further, TEM micrographs results showed that Cr stress alone significantly ruptured the plant cell organelles of both cultivars by increasing the size of starch grain and the number of plastoglobuli, damaging the chloroplast and mitochondrion structures. However, exogenously applied SA significantly recovered these damages in the plant cells of both cultivars. It was also observed that cultivar ZS 758 was proved to be more tolerant under Cr toxicity. Gene expression analysis revealed that combined treatments of Cr and SA increased antioxidant-related gene expression in both cultivars. Findings of the present study demonstrate that SA induces the enzymatic antioxidant activities and related gene expression, secondary metabolism, and improves the cell structural changes and the transcript level of specific stress-associated proteins in root and leaf of two oilseed rape cultivars under Cr toxicity.