Highlights • The water stress had a negative effect on the photosynthetic parameters, stomatal characteristics. • The SOD activities which in leaves were higher than in roots, there was the opposite result in POD, CAT. • The fitting model based on different growth periods was established, the fitting result was well. • Furthermore, the fitting model of each growth period, especially, was better than that of the whole growth periods. • he effect of moderate water stress on physiological indexes was higher than mild water stress in the same growth period. Abstract The aim of this study is to investigate the response of physiological functions, and to establish the model between net photosynthetic rate and some other physiological indexes during the eighteen water stress days and the three subsequent re-water days in different growth periods of tomato. Our data showed that the most of the photosynthetic indicators had the decline trend under water stress, and the value under mild water stress was higher than that of moderate water stress at the same growth stage. Furthermore, all of them recovered to the initial value by and large eventually. There was a significant positive linear relationship between net photosynthetic rate and transpiration rate, net photosynthetic rate and stomatal conductance. The instantaneous water use efficiency peaked at the last day of water stress. The activities of superoxide dismutase, peroxidase and catalase in both tomato leaves and roots increased continuously under water stress conditions at three growth stages and recovered a lot after rehydration. According to the results, the superoxide dismutase activities in leaves was higher than in roots and the peroxidase, catalase activities in leaves was lower than in roots throughout the whole growth periods. The value of net photosynthetic rate reduced with the increasing of antioxidant enzyme activities in the whole growth periods, and the correlation between net photosynthetic rate and antioxidant enzyme activities was highly significant. Both the stomatal length and stomatal width had a decline trend which was differ from the stomatal density, stomatal density increased during the water stress days. There was a positive linear correlation between net photosynthetic rate and stomatal length (significant), and significant quadratic relationship between net photosynthetic rate and stomatal width; on the contrary, the negative linear correlation between net photosynthetic rate and stomatal density was highly significant. Although the water stress had negative influences on physiological indicators of tomato, the effects of water stress on physiological indexes was not irreversible, since these indexes had restored to a certain extent after rehydration. The water stress had a bigger impact on physiological parameters in anthesis period than the seedling and fruit expanding period. In conclusion, it was verified that mild water stress had no significant effect compared to the full irrigation on tomato physiological indexes during non-critical growth periods (seedling and fruit expanding period). What's more, the relationship between net photosynthetic rate and other physiological indexes can be predicted with the data of whole growth period, but it is better to use the data of each growth period for the accurate prediction. [ABSTRACT FROM AUTHOR]