Uniform scions and rootstocks should be produced to ensure grafting success. Light quality is an important environmental factor that regulates seedling growth. The effects of warm- and cool-white light emitting diode (LED) ratios on seedling growth were investigated. Scions and rootstocks of cucumber, tomato, and watermelon were grown in a closed transplant production system using LED as the sole lighting source. The LED treatments were W1C0 (only warm-white), W1C1 (warm-white: cool-white = 1:1), W3C1 (warm-white: cool-white = 3:1), and W5C2 (warm-white: cool-white = 5:2). The seedlings grown in W1C1 had the shortest hypocotyls, and the seedlings grown in W1C0 had the longest hypocotyls among the three tested vegetables. The hypocotyls of watermelon scions, watermelon rootstocks, and tomato rootstocks were shortest in W1C1, followed by those in W3C1, W5C2, and W1C0, but there was no significant difference between W3C1 and W5C2, which remained the same as the ratio of cool-white LEDs increased. In addition, tomato scions had the first and second longest hypocotyls in W1C0 and W3C1, respectively, and the shortest hypocotyls in W5C2 and W1C1, along with W5C2 and W1C1, although the difference was not significant. The stem diameter was highest in W1C0 except for tomato seedlings and rootstocks of watermelon. The shoot fresh weight of scions and rootstocks of cucumber and watermelon and the root fresh weight of cucumber scions were lowest in W1C1. These results indicated that different ratios of LED lighting sources had a strong effect on the hypocotyl elongation of seedlings.