In order to quantitatively analyze the issues on the mutual use of water and the mechanism of salt migration, clear the relative competitive between the two species of intercropping in wheat-sunflower intercropping system in Hetao irrigation area, the experiment was conducted based on root separation method. The results showed that in wheat-sunflower intercropping system, the wheat utilized 78.23~94.23m3/hm2 of water by the side of sunflower. Meanwhile, the sunflower utilized 44.96~57.97m3/hm2 of water by the side of wheat. By the cross superposition effect of soil internal space, more soil water of 18.56~42.84m3/hm2 and 20.79~46.63m3/hm2 in wheat and sunflower belts may be utilized, the mean value of root soil EC in wheat and sunflower belts could be reduced by 1.32%~4.64% and 2.26%~3.16%, respectively. By the water and nutrient complementarity effect of soil internal space, more soil water of 15.12~26.40m3/hm2 and 47.60~57.44m3/hm2 in wheat and sunflower belts may be utilized, the mean value of root soil EC in wheat and sunflower belts could be reduced by 2.98%~4.69% and 1.82%~2.44%, respectively. For the relative competitive ability between the two species in intercropping system, the wheat was stronger than sunflower, limiting the cross superposition effect and water and nutrient complementarity effect of root in intercropping system was conducive to upgrading the relative competitive ability between the two species of sunflower.