Salt stress affects the physiological processes and morphological structure of plants, thereby inhibiting plant growth and development and reducing the fruit yield and quality. Most cherry rootstocks are sensitive to excessive salt and alkaline conditions. Salicylic acid (SA) plays a role in the response to various abiotic stresses. To determine the effects of SA on the resistance of cherry rootstocks to salt stress, a salt environment was simulated by watering with a 100-mM NaCl solution and then spraying leaves with 1.0-mM SA. Salt treatment significantly decreased the photosynthetic rate (Pn) and ratio of variable fluorescence to maximum fluorescence (Fv/Fm) of cherry rootstocks, whereas SA application increased the Pn and Fv/Fm in the salt stress with SA-treat group. Meanwhile, SA reduces the accumulation of Na+ and H2O2 in leaves. Additionally, the activities of antioxidant enzyme (peroxidase, catalase, and superoxide dismutase) were increased under salt stress, and this increase was more obvious under salt stress with SA application treatment, indicating SA contribution in improving the salt tolerance. RNA-seq analysis of cherry rootstocks treated with 1.0-mM SA, 100-mM NaCl, and both 1.0-mM SA with 100-mM NaCl, revealed 537, 298, and 521 significantly differentially expressed genes (DEGs), respectively. The main DEGs were phytohormone-related genes, stress-related transcription factors, Ca2+ signaling-related genes, and other functional protein-related genes. Overall, our study contributes to the understanding of the molecular mechanisms of SA-induced salt tolerance in cherry rootstocks.