The effects of waterlogging stress on the growth, chlorophyll and MDA content of cucumber seedlings were studied by using cucumber varieties (Cucumis sativus L. cv. Jinyan No.7) as materials. The results show that plant height, leaf number, shoot fresh weight, total root length, total projected area and total surface area of cucumber seedlings showed insignificant differences with those of the control; root fresh weight, root average diameter, total root volume were significantly higher, but the number of root tips and furcation number increased first and then reduced; the chlorophyll content of cucumber seedlings was significantly lower than that of control; MDA content was significantly higher than that of control under waterlogging stress. It was showed that the cucumber was tolerant to waterlogging stress, but the ability of waterlogging stress was limited, and the physiological was significantly hurt and photosynthesis of cucumber seedlings was significantly affected by waterlogging stress.