Background and Aims <p>The photosynthetic adaptation mechanism of salt tolerance in plants is complex and still not completely understood. This study aims to elucidate the salt tolerance mechanism related to photosynthetic apparatus and carbon metabolism in tomato seedlings.</p> Methods <p>A hydroponic experiment compared the response differences in the structure and function of photosystem I (PSI) and photosystem II (PSII) of tomatoes with varying salt tolerance after salt stress. The activity and transcript level of enzymes related to Calvin cycle and sugar metabolism were investigated.</p> Results <p>Salt stress inhibited the activity of PSII and PSI in both tomato varieties, as evidenced by suppressed electron transfer efficiency, multiple damaged sites on the donor and receptor sides of PSII, and disturbed energy flow distribution. Additionally, salt stress inhibited the carbon assimilation efficiency of both tomato varieties, as indicated by reduced activity and transcript levels of key enzymes related to Calvin cycle. However, salt stress activated defense strategies including heat dissipation protection mechanism, optimized light energy allocation of PSII, and sugar-dependent osmotic regulation. The salt tolerance of salt-resistant variety was mainly attributed to higher carbon assimilation efficiency and sugar accumulation and its ability to protect PSII structures to a certain extent and maintain better PSI electron transfer.</p> Conclusion <p>These results demonstrated that the structure of PSII, PSI activity, carbon assimilation efficiency, and sugar accumulation play important roles in improving salt resistance of tomato. This study helped in understanding the salt tolerance mechanism of tomato, which can contribute to the efficient breeding of salt-tolerant varieties.</p>