The invention discloses a watermelon tissue culture seedling grafting method, comprising the following steps: stock preparation, scion preparation, grafting, grafted seedling culturing, grafted seedling transpiration and the like. Stock seeds are sowed in a nutrition disc after pregermination, and can be grafted after two leaves and one bud grow; 2-3cm-high watermelon tissue culture seedlings are domesticated and subjected to scion ingraftment, and grafted through a top grafting method; the grafted seedlings are subjected to timely heat preservation, humidity preservation, shading culturing, and shoots of stock are timely removed; and the grafted seedlings with two leaves and one bud can be transplanted into the land for growing field crops and subjected to field management as same as common grafted seedlings. According to the invention, rooting is avoided in the tissue culture seeding culturing, the problem of difficulty in rooting or instability can be overcome by directly obtaining the watermelon grafted seedlings; the method can be carried out all the year round with artificially controlling conditions, is short in period, high in rate of survival, simple and feasible and convenient to operate, the production cost of the watermelon grafted seedlings is reduced, and the problems of imperfect regeneration plant rooting effect and low transportation survival rate during watermelon tissue culturing are solved.