This study aims at discovering the relations of water and fertilizer coupling with the growth and water use efficiency of watermelon cultivated by organic substrate in order to provide a theoretical basis for high-efficient production of watermelon in greenhouse. Watermelon variety ‘Sumi 8’ was used, three irrigation levels and four fertilization levels were designed. The results showed that maximum yield and plant biomass were obtained in middle irrigation level (60 L) and (20-10-30) g (N-P₂O₅-K₂O) fertilization level. There were strongly synergistic effects between water and fertilizer on yield and plant root biomass of watermelon (P<0.05), and the effects were in order of fertilization > water > interaction. Water use efficiency of watermelon was reduced with the increasing of irrigation levels, but increased with the increasing of fertilizer under the same irrigation levels. The interaction effects of water and fertilization on photosynthetic characters of watermelon leaves were significant in different growth periods (P<0.05), but only significant on transpiration rate in the expansion period of watermelon.