Under the condition of cotton-wheat intercropping system, with the application of three root separating ways, i.e. in the wheat-cotton intercropping system, the wheat roots mixed with cotton roots naturally (WCRM), the wheat roots was separated from cotton roots by nylon net (WCRN) and the wheat roots was separated from cotton roots by plastic film(WCRP). Effect of different composite root on soil microorganism population, soil bacterial activity and soil nutrient content in the cotton rhizosphere and non-rhizosphere was studied. The results showed that: in the coexist period of wheat and cotton, soil bacteria number in the cotton rhizosphere and non-rhizophere in WCRM was the highest, followed gradually by in WCRN and in WCRP. But fungi and actinomyces number in WCRM were the lowest. In a word, WCRM was in favor of increasing the microorganism population in the cotton rhizosphere and non-rhizosphere, and subsequently result in increasing of the vigor of the soil microorganism in WCRM, which leading to the increase of content on total nitrogen, available phosphorus and rapidly available potassium. As the nylon net and the plastic film can alleviate or interrupt the nutrient competition between wheat roots and cotton roots, the soil nutrient content in the cotton rhizosphere of WCRM was the lowest, and in WCRN that was the highest. In budding stage, as wheat had been harvested, the soil nutrient content in cotton rhizosphere and non-rhizosphere in WCRM was improved, that was the content of total nitrogen, available phosphorus and rapidly available poassium were higher in WCRM than in the two others. As a whole, in WCRM, there not only existed disadvantages as nutrition competition between belowground tissues of wheat and cotton, but also existed advantages in improving soil microorganism activity and soil nutrient content at the cotton rhizosphere and non-rhizosphere as affect by the wheat root.