Abiotic stress, such as salinity, affects the photosynthetic apparatus of plants. It is reported that the use of selenium nanoparticles (Se NPs), and biochemical compounds such as chitosan (CS) increase the tolerance of plants to stress conditions. Therefore, this study aimed to elucidate the potential of Se NPs, CS, and their composite (CS + Se NPs) in improving the photosynthetic apparatus of C. sinensis under salt stress in greenhouse conditions. The grafted seedlings of C. sinensis cv. Valencia after adapting to the greenhouse condition, were imposed with 0, 50, and 100 mM NaCl. After two weeks, the plants were foliar sprayed with distilled water (control), CS (0.1% w/v), Se NPs (20 mg L− 1), and CS + Se NPs (10 and 20 mg L− 1). Three months after treatment, the levels of photosynthetic pigments, leaf gas exchange, and chlorophyll fluorescence in the treated plants were evaluated.