Abstract: The allelopathic effect of root exudates is quite common in soil and other media, and the effect due to the stress of continuous cropping often affects the root growth and yield of companion crops. This experiment, conducted under controlled environments, was to investigate the eugenol and intercropping effects on the root growth characteristics and yield of wheat (Triticum aestivum) under three water (75%, 60% and 45% of field capacity) supply conditions. Eugenol (2-methoxy-3-propenylphenol) exudates from wheat roots were used as the trial allelochemical. Results showed that eugenol at the rate of 300×10^-6 mol/kg of soil negatively affected root volume, root dry weight and root length of wheat crops. The negative effect of eugenol on wheat roots enhanced with a decrease of irrigation rate. There were significant differences between the 75% and 45% water supply levels. The negative effect on root volume, root length and root dry weight of intercropping wheat at 75% water supply conditions were lower by 54.69%, 26.70%, and 18.67% respectively than at 45% water supply conditions, and lower by 33.32%,49.55%, and 55.41% respectively in a monocropping system. In contrast, the wheat/soyabean intercropping system significantly weakened the allelopathic effect with little negative effect on root growth characteristics of wheat under the same water supply conditions. Cropping systems and water supply significantly affected root dry weight which then had a significantly positive impact on grain yield of wheat. This study demonstrates that the negative allelopathic effect, often occurring with continuous cropping, can be weakened through optimizing cropping systems and improved water management.