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Background Excessive and insufficient application of N fertilizer can inhibit plant growth, reduce N-use efficiency (NUE) and lead to production reduction. Watermelon is an important crop that often restricted by inappropriate N supply. The study aims to test whether grafting with bottle gourd rootstock can improve NUE and growth performance of watermelon under low N and to clarify the underlying physiological mechanism. Methods Grafted (self-grafted and rootstock-grafted watermelon) and ungrafted (watermelon and bottle gourd) seedlings were tested respectively, and treated with 9 mM (normal condition) and 4 mM (low N condition) NO3--N concentrations for 18 days under hydroponic conditions.Results The growth and NUE of bottle gourd rootstock-grafted watermelon seedlings increased under low-nitrate, while decreased slightly in self-grafted seedlings compared with control. Rootstock-grafted plants had higher root morphological characteristics, NO3- uptake, photosynthesis, and NUE traits than self-grafted plants under low-nitrate. The expression of nitrate transporter genes NRT1.5 and NRT2.1, and N metabolizing enzyme genes NR, NiR, GS1 and GS2 of rootstock-grafted plants were significantly up-regulated at low-nitrate treatment, which may lead to increased NO3- uptake and metabolism.Conclusion The bottle gourd rootstock grafting can improve the growth and NUE of watermelon seedlings under low-nitrate treatment. The improved plant performance is attributed to the vigorous root systems and higher NO3- uptake of rootstock roots, and the enhanced N metabolism and photosynthetic capacity of scion leaves. Grafting with the bottle gourd rootstock may be beneficial to the efficient production of watermelon and economic application of N fertilizer.