Illumination during storage was proven to extend the storability of seedlings, but little attention has been given to the underlying mechanism. To determine how light conditions affect photosynthetic status in watermelon [Citrullus lanatus (Thunb.) Matsum. and Nakai] plug seedlings, differences of stomatal development and relative photosynthetic characteristics of expanding new leaves when stored for 8 days at 15 °C in light at a photosynthetic photon flux (PPF) of 15 μmol·m−2·s−1 or darkness were investigated. The stomatal density (SD) increased with time to a peak and then decreased from the start of storage in light to the subsequent transplantation. Dark storage retarded the stomatal development and delayed the appearance of the peak of SD. Compared with those under dark storage, light-stored seedlings showed significantly higher SD and stomatal index (SI) in leaves accompanied by higher maximal photochemical efficiency of PSII (Fv/Fm) and quantum yield of PSII (ΦPSII). During storage in darkness, Fv/Fm and ΦPSII declined steeply with increasing storage duration but recovered gradually to reach the same level of those in light at the fourth day after transplanting. Seedlings stored in light for 8 days showed higher net photosynthesis rate (Pn), stomatal conductance (gS), intercellular CO2 concentration (Ci), and transpiration rate (Tr) than in darkness. The post-storage recovery of Pn, gS, and Tr were closely related to the SI, which ensured the fast recovery of photosynthesis during the early stage of transplanting. In agreement with the change of SD, no differences in Pn, gS, Ci, and Tr between light and dark storage were observed after 8 days of transplantation. Seedlings stored in light appeared vigorous and the shoot dry weight was significantly higher than that of dark-stored ones. Although seedlings in dark storage had a poor appearance during storage, they showed inhibited regrowth potentials during the subsequent transplanting stage. This study exhibited that light in short-term storage contributed to maintaining stomatal development as well as photosynthetic efficiency in watermelon, which could also extend to post-storage for ensuring the transplant quality of seedlings after removal from storage.