Salt stress affects the growth, metabolism, yield, and quality of crops. To adapt to high-salt environments, plants form various regulatory mechanisms. Salt over sensitive (SOS) is the key gene of SOS signal transduction pathway. As a member of the SOS3 subfamily, the function of SOS3-3 under salt stress has not been reported. To verify the function of SOS3-3 and the morphological and physiological parameters, the expression of genes related to stress were compared between the SOS3-3 overexpressed (OESOS3-3) and silenced tomato (VSOS3-3) at control and 10 days' NaCl treatment. The results showed that, compared with the control (Ve), the plants of VSOS3-3 were shorter under salt stress, with curled leaves and abscission. The fresh and dry weights, Fv/Fm, total chlorophyll content, antioxidant enzyme activities, and proline content of VSOS3-3 significantly decreased, while the relative conductivity, hydrogen peroxide (H2O2), and Malondialdehyde (MDA) content of VSOS3-3 plants significantly increased compared to that of WT, respectively. Compared to the wild-type (WT), OESOS3-3 plants were less damaged by salt stress, with significantly higher plant height, fresh and dry weights, Fv/Fm, total chlorophyll content, antioxidant enzyme activity, and proline content. However, the relative conductance, H2O2, and MDA content were significantly lower in OESOS3-3 than WT. The expression levels of SOS1, SOS2, LKT1 (ion transport-related gene), APX1 (ROS signaling pathway-related gene), P5CS (osmoregulation-related gene), and ABF4 (ABA signaling pathway-related gene) were significantly lower in VSOS3-3 than Ve, but significantly higher in OESOS3-3 than in WT. These results suggested that SOS3-3 regulate salt tolerance by influencing physiological and biochemical changes and the expression of genes related to stress response. This study revealed the mechanism of SOS family participating in regulating tomato salt tolerance, providing a theoretical basis for improving tomato salt tolerance.