Through the method of traditional culture and PCR-DGGE, variety of soil microbial structure in continuous cropping cotton fields in south Xinjiang was analyzed. The results showed with the increase of continuous cropping years, the number of bacteria and fungi, ratio of total bacteria and fungi and Shannon-Weiner index increased at first, than decreased, and after continuous cropping 15 years increased again, it was a lower point in the sample of continuous cropping cotton 15 years. Bacterial diversity and structure changed slightly, while the quantity and species of dominant bacteria were not much different in the fields with different continuous cropping years. Compared with bacteria, fungi structure was more sensitive to continuous cropping years, dominant fungi population presented a single tendency and lower species diversity.