Seeds of triploid watermelon cultivar ‘Heiniu’ and diploid watermelon cultivar ‘Heibao’ were used to investigate the morphology of seeds, the influence of seed coat on permeability of the seed and the ultra structure of seed coat. The results showed that the average thickness of the sclerotesta of the triploid was almost 2 times thicker than that of the diploid and there was a sclerosis with cells densely arranged in triploid but not diphoid watermelon seed. The average thickness of the endotesta of the triploid was almost 10 times thicker than that of the diploid. The endotesta of triploid watermelon was lignified and the complicated structure consisted of 3 layers. During germination, the structure changes of endotesta between the two kinds of watermelon seed coat were significant. And the sclerotesta and endotesta of triploid watermelon seed blocked the water and air exchange between the embryo and the outside environment to some extent, which hindered the imbibition and germination of triploid watermelon seed. But the seed coat of the diploid watermelon didn’t block the air exchange.