Background: Excessive 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 the NUE and growth performance of watermelon under reduced nitrate application and to clarify the underlying mechanism.Methods: Grafted (self-grafted and rootstock-grafted watermelon) and ungrafted (watermelon and bottle gourd) seedlings were treated separately with 9 mM (control) and 4 mM (reduced-nitrate) N concentrations for 18 days under hydroponic conditions.Results: The growth and NUE of bottle gourd rootstock-grafted watermelon seedlings increased under reduced-nitrate, while decreased slightly in self-grafted seedlings compared with the control. Rootstock-grafted plants had higher root morphological traits, NO3− accumulation, NR and GS activities, photosynthesis, and NUE traits than self-grafted plants under reduced-nitrate. Reduced-nitrate treatment significantly up-regulated the expression of nitrate transporter genes NRT1.5 and NRT2.1 and N metabolizing enzyme genes NR2, NR3, NiR, GS1 and GS2 in rootstock-grafted plants.Conclusion: Under reduced-nitrate treatment, grafted watermelon can make better use of the developed rootstock roots to increase the NO3− absorption and transportation to the shoot, so as to enhance the N metabolism potential and photosynthetic capacity of scions, and finally improve plant growth and NUE. The enhanced NO3− uptake and utilization of rootstock-grafted plants were regulated at the transcriptional level. Grafting with the bottle gourd rootstock may be beneficial to the efficient production of watermelon and economic application of N fertilizer.