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Background Application of exogenous glycine betaine (GB) and exogenous salicylic acid (SA) mitigates the adverse effects of salinity. Foliar spraying with exogenous GB or SA alleviates salt stress in plants by increasing leaf gas exchange and stimulating antioxidant enzyme activity. The effects of foliar application of exogenous GB and SA on the physiology and biochemistry of cotton seedlings subjected to salt stress remain unclear. Results Results showed that salt stress of 150 mM NaCl significantly reduced leaf gas exchange and chlorophyll fluorescence and decreased photosynthetic pigment quantities and leaf relative water content. Foliar spray concentrations of 5.0 mM exogenous GB and 1.0 mM exogenous SA promoted gas exchange and fluorescence in cotton seedlings, increased quantities of chlorophyll pigments, and stimulated the antioxidant enzyme activity. The foliar spray also increased leaf relative water content and endogenous GB and SA content in comparison with the salt-stressed only control. Despite the salt-induced increase in antioxidant enzyme content, exogenous GB and SA in experimental concentrations significantly increased the activity of glutathione reductase, ascorbate peroxidase, superoxide dismutase, catalase and peroxidase, and decreased malondialdehyde content under salt stress. Across all experimental foliar spray GB and SA concentrations, the photochemical efficiency of photosystem II (FV/FM) reached a peak at a concentration of 5.0 mM GB. The net photosynthetic rate (Pn) and FV/FM were positively correlated with chlorophyll a and chlorophyll b content in response to foliar spraying of exogenous GB and SA under salt stress. Conclusions We concluded, from our results, that concentrations of 5.0 mM GB or 1.0 mM SA are optimal choices for mitigating NaCl-induced damage in cotton seedlings because they promote leaf photosynthesis, increase quantities of photosynthetic pigments, and stimulate antioxidant enzyme activity. Among, 5.0 mM GB and 1.0 mM SA, the best performance in enhancing endogenous GB and SA concentrations was obtained with the foliar application of 1.0 mM SA under salt stress.