Grafting is an effective way to increase plant tolerance to biotic and abiotic stressors, it is widely used in watermelon production. However, grafting is labor intensive due to the additional time is required, such as the management of rootstock regrowth. This study used a new grafting tool to destroy (remove) the epidermis of pumpkin and bottle gourd rootstock cotyledon base during grafting, we called this a new grafting method. Compared with the traditional grafting (100%), the new grafting method had significantly lower rate of rootstock regrowth (2-23%), higher watermelon scion dry weight and leaf area. In addition, the time used for the new hole insertion and one cotyledon grafting method to destroy (remove) the epidermis of rootstock cotyledon base (4.2 s/plant, 4.2 s/plant) is significantly shorter than the time required to remove the rootstock regrowth manually in the traditional grafting (9.3 s/plant, 8.8 s/plant). Thus, this study developed a new grafting method for watermelon to inhibit rootstock regrowth and enhance scion growth, and this new method is cost-effective for grafted watermelon seedlings.