Watermelon is susceptible to wilt disease under continuous monocropping management. Watermelon/aerobic rice intercropping can alleviate watermelon wilt disease in continuous management soil. However, the mechanism is not very clear. A pot experiment was carried out to investigate effects of watermelon/aerobic rice intercropping on composition and contents of watermelon root exudates, such as phenolic acids amino acids and organic acids. Results show that watermelon wilt disease was alleviatedunder watermelon/aerobic rice intercropping condition. Compared with control, the treatment of inoculation with FON (Fusarium oxysporum f. sp. niveum）significantly increased the content of phenolic acids in the root exudates, especially coumaric acids, while the treatment of watermelon/aerobic rice intercropping reduced the exudation of most phenolic acids. Even in pots inoculated with FON, watermelon/aerobic rice intercropping significantly reduced the content of phenolic acids in the root exudates. Compared with control, FON inoculation increased the content of amino acids in watermelon root exudates, but did not in pots under watermelon/aerobic rice intercropping condition. And FON inoculation also increased significantly the volume of organic acids in watermelon root exudates, whereas watermelon/aerobic rice intercropping reduced the exudation of most of the organic acids and even in pots inoculated with FON. In conclusion, watermelon/ aerobic rice intercropping may alleviate watermelon wilt disease, which is held to be related to the variation of the composition and volume of the exudates from watermelon roots.