Graft healing is an important factor that determines the survival of the double-root-cutting (DRC) grafted plants. Recent studies have shown that adding far-red light (FR) to change the red/far-red (R/FR) ratio plays a crucial role in plant growth and development. However, there have been few studies on how R/FR ratio affects the grafting union healing process of DRC grafted seedling. In this study, we applied four light quality treatments: dark (D), white (R/FR=6.0, W), R/FR ratios of 3 (H) and 0.3 (L). The effects of different ratios of R/FR on the survival rate, photosynthetic fluorescence characteristics, graft union healing and growth of DRC grafted watermelon seedlings during the healing period were analyzed using darkness (D) as a control. The results showed that compared with the control L treatment could significantly improve the survival rate, growth indicators and photosynthetic capacity of grafted seedlings, significantly increased the activities of SOD and POD, and contents of soluble sugar and protein in the graft union, and significantly reduced the accumulation of O2−, H2O2 and MDA, which was conducive to the production of callus cell and the healing of grafted union. Meanwhile, qRT-PCR results showed that the expression levels of graft healing-related genes, ClaIAA, ClaSOD, ClaPOD, ClaWOX4, ClaGH9B14 and ClaGH9B1 were significantly induced L treatment. The current study can contribute to speeding up the development of industrialized production with high-quality watermelon grafted seedlings.