Low-temperature storage in darkness is usually used for preserving seedlings for a short period. To investigate whether grafted watermelon [Citrullus lanatus (Thunb.) Matsum. and Nakai] seedlings are superior to non-grafted ones under low-temperature storage in darkness and to study their physiological differences during storage, watermelon (‘Zaojia 84-24’) scions were grafted to pumpkin (Cucurbita moschata Duch. ‘Zhuangshi’) rootstocks. Carbohydrate levels; chlorophyll and malondialdehyde contents; the activities of superoxide dismutase, catalase, and peroxidase; and photochemical efficiency were assayed during 6 days of storage at 15 °C in darkness. After that, seedlings were transplanted into an artificial climate chamber. The net photosynthetic rate and stomatal conductance (gS) were measured on the first and third days after transplanting. The results showed that the grafted watermelon seedlings had more soluble sugar and chlorophyll contents, higher activities of antioxidant enzymes, and less malondialdehyde content than the non-grafted ones after 6 days of storage. In addition, low-temperature storage in darkness damaged the photosystem II of non-grafted watermelon seedlings more than that of grafted ones. After transplanting, grafted seedlings had a higher net photosynthetic rate. The results suggest that grafted watermelon seedlings were more suitable for the low-temperature storage in darkness than the non-grafted ones.