This study investigated effect of various durations of contton cropping on microbial community diversity of rhizosphere soil in south and north parts of Xinjiang by Biolog method, cultured-based microorganism and soil enzyme measurements. Biolog analysis showed that there were significant differences in microbial carbon utilization and functional diversities of microbial community of rhizosphere soils under various durations of contton cropping. Soil microbial activity of uncultivated soils were lower than that of cultivated soils. The AWCD of rhizosphere microbial community and Shannon(H) index were higher under 5-10 years than under 15-20 years of continuous contton cropping. The principal component analysis showed that there was significant differences in carbon utilizations of soil microbial community. The significant differences existed on PC1 and PC2, respectively, between cultivated and uncultivated soils in group one and group two, and the coefficients of uncultivated soils were negative,those of cultivated soils were positive. However significantly differences in PC1 were found between soils under rotation system and continuous cotton cropping.The differences of carbon sources in PC1 were mostly caused by carboxylic acid and polymers, which were probably the main carbon sources affectting soil microbial community under continuous cotton cropping.The results of count of soil culturable microorganism showed that numbers of bacteria in the uncultivated soils were less than that in the cultivated soils. Nevertheless, numbers of bacteria were larger under 5-10 years than under 15-20 years of continuous contton cropping. The numbers of fungi increased after 15-20 years continuous contton cropping. However, numbers of Actinomyces did not change obviously between cultivated and non-cultivated soils. Soil enzyme activities were decreased significantly after 5-15 years of continuous contton cropping, then, increased after 15-20 years of continuous contton cropping. It is concluded that soil microbial community diversities were decreased in rhizosphere soils under long-term continuous cotton cropping, and this might be the main cause of yield decrease of cotton in Xinjiang.