In this experiment, two cherry tomato varieties, ‘Hongfei 6’ (HF) of waterlogging tolerance type and ‘Qianxi’ (QX) of sensitive type, were used as the materials, with normal moisture as the control (CK). Six flooding depth, respectively ?10 cm, ?5 cm, ?2 cm, 0 cm, 2 cm, 5 cm (D10, D5, D2, W0, U2, U5) was used to determine the growth, physiological and biochemical indicators of cherry tomato seedlings under different treatment to explore the response of cherry tomato at seedling stage to different flooding depths. Flooding treatment could inhibit the growth of plant height, stem thickness, dry matter weight, root length, root diameter, root surface area and root volume compared with CK. With the increase of flooding depth, plant height, dry matter mass, root length, root diameter, root surface area and root volume were inhibited more obviously, and the effects of W0, U2 and U5 were significantly lower than that of CK, while there was no significant difference in plant height, stem diameter and mean root diameter between D10, D5 and CK. The content of malondialdehyde (MDA), soluble sugar and proline gradually increased with the increase of the flooding depth. The activity of superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD) also showed a tendency to gradually increase with the increase of flooding depth, and from 2 to 6 days, the effects of D2, W0, U2, and U5 were higher than that of CK. After 14 days of flooding, the activity of SOD and CAT of QX of W0, U2 and U5 were significantly lower than those of CK. Correlation analysis revealed that MDA, POD, CAT, soluble sugar and proline were significantly positively correlated. Therefore, flooding depth was also an important factor for flood damage. Higher flooding depth would lead to greater damage to cherry tomatoes. 5 cm below the cherry tomato planting surface was the flooding depth threshold.