To investigate the regulatory effect of salicylic acid(SA) on the growth of watermelon seedlings under flooding stress, the ‘Xuelong 1’ watermelon variety was used as material. Six concentrations(0.0, 0.5, 1.0, 1.5, 2.5, 3.5 mmol/L) of SA solution were sprayed, and the growth of watermelon seedlings, root system configuration, photosynthetic parameters, chlorophyll content, SPII light energy conversion efficiency, antioxidant enzyme activity and other indicators under flooding stress were measured and then were subjected to the principal component analysist analyze the effects of SA treatment on the physiological characteristics of watermelon seedlings under flooding stress. The results showed that different concentrations of SA alleviated the adverse effects of flooding stress on watermelon seedlings, and increased the activities of chlorophyll content, carotenoid content, actual photochemical efficiency of PSⅡ, superoxide dismutase (SOD), catalase(CAT), peroxidase(POD), and decreased the MDA content, of watermelon seedlings under flooding stress. It could be concluded that exogenous SA could improve the flooding tolerance of watermelon seedlings. Compared with 0.0 mmol/L SA treatment, under 1.0 mmol/L SA treatment the plant height, stem thickness, fresh mass and dry mass of watermelon seedlings were significantly increased by 18.80%, 34.74%, 23.57% and 67.27%, respectively; the total root length and the number of root tips were significantly increased by 116.41% and 101.25%, respectively; and the content of chlorophyll a, chlorophyll a+chlorophyll b and carotenoids were increased by 66.55%, 67.46% and 73.81%, respectively; CAT activity increased significantly by 20.92% and MDA content decreased significantly by 53.32%. The results of principal component analysis showed that waterlogging tolerance of watermelons treated with 1.0, 1.5, 2.5, 0.5, 3.5 and 0.0 mmol/L SA decreased successively.