Abstract: The soil microorganism quantities and enzyme activities were studied in fields under the wheat-cotton intercropping and garlic-cotton intercropping systems. The results show that compared with the cotton monoculture, both garlic cotton intercropping and wheat cotton intercropping are conductive to the proliferation of soil bacteria and actinomycetes and inhibit the proliferation of fungi, and the effects of the garlic-cotton intercropping system are more pronounced than those of the wheat-cotton intercropping system. The soil urease activity and sucrase activity in 020 cm soil layer in the whole growth period of the garlic-cotton intercropping system are significantly higher than those of the cotton monoculture, and the alkaline phosphatase activity of the garlic-cotton intercropping system is significantly higher than that of the cotton monoculture except the flowering and blooming stage of cotton. The catalase activities of the garlic-cotton intercropping system at the seedling stage and boll opening stage are significantly higher than that of the cotton monoculture. The soil urease activities and sucrase activities in 020 cm soil layer at the seedling, flowering and boll stages of the wheat-cotton intercropping system are higher than those of the cotton monoculture, the alkaline phosphatase activity at the bud stage is significantly higher than that of the cotton monoculture, and the catalase activity at the seedling and boll opening stages are significantly higher than those of the cotton monoculture. In conclusion, the garlic-cotton intercropping and wheat -cotton intercropping systems can increase the quantities of soil bacteria and actinomycetes which suppress the occurrence of cotton cropping obstacles effectively, and can increase the activities of soil-related enzymes which are good for creating healthy soil in cotton fields.