Photosynthesis is the sole source of crop yield, so to understand salt resistance mechanism of photosynthetic apparatus is of paramount importance in improving salt resistance of crop. In this study, in order to explore the different salt resistance mechanisms of photosynthetic apparatus between a salt resistant wild soybean (Glycine soja Sieb. et Zucc. ZYD 03262) and a salt sensitive cultivated soybean (Glycine max (L.) Merr. Shanning 11), we investigated the responses of whole plants and detached leaves of the two soybean plants under treatments with different NaCl concentrations (0, 100, 200 mmol/L). The results shown that the photosynthesis (Pn), the maximum photochemical efficiency of PSⅡ (Fv/Fm), the actual photochemical efficiency of PSⅡ (Φ_PSⅡ), the chlorophyll content as well as plant growth were all decreased in the two soybean plants by the treatments with different concentrations of NaCl. However, the inhibition of the NaCl on photosynthetic apparatus was more severe in the cultivated soybean than in the wild soybean. The Na⁺ contents and the ratio of Na⁺/K⁺ in leaves of the wild soybean plants were significantly lower than those of the cultivated soybean, while the Na⁺ contents in roots of the wild soybean were higher than those of the cultivated soybean, which indicates that the wild soybean can prevent more Na⁺ from getting into photosynthetic mesophyll cells. This fact may partly account for the less inhibition of the photosynthetic apparatus in the wild soybean plant under NaCl stress. To elucidate whether the photosynthetic apparatus of the wild soybean is more tolerant to Na⁺ in photosynthetic mesophyll cells, detached fully expanded leaves of the two soybean plants were directly subjected to NaCl solution to eliminate the difference in their selective effects of Na⁺ in their roots and stems. It is unexpectedly noticed that the Fv/Fm, the Φ_PSⅡ, the active PSⅡ reaction centers per excited cross section (RC/CS) and the photochemical performance index (PI) decreased more significantly in detached leaves of the wild soybean than those of the cultivated soybean. The ion analysis showed that the Na⁺ contents in detached leaves of the wild soybean were higher than those of the cultivated soybean when the detached leaves were treated with 100 and 200 mmol/L NaCl. These results demonstrate that the photosynthetic apparatus in the wild soybean is not more salt tolerant than in the cultivated soybean. It is the lower Na⁺ contents in photosynthetic mesophyll cells of the wild soybean plant under NaCl stress that ensure the photosynthetic apparatus in the wild soybean to retain higher photosynthetic performance under salt stress, which is one of the mechanisms to keep higher salt resistance in the wild soybean than in the cultivated soybean.