Cotton production plays an important role in the local economy of Xinjiang, China. According to traditional theory, long-term continuous cotton cropping will inevitably lead to unbalance in soil nutrients and diminish soil fertility. In 2008, soil samples, as 0-20 cm layers, were collected from native land (without cultivation, as a control) and five continuous cropping cotton fields, with different cultivation times (3, 8, 12, 20 and 30 years, respectively). Based on the analysis of seven physical and chemical properties: soil water content, bulk density, pH, organic matter, total N, available P, and available K, and five soil enzymatic activities: catalase, polyphenol oxidase, urease, invertase, and alkaline phosphatase, this study attempts to evaluate soil quality across continuous cropping cotton fields for different years in the Aler reclamation area of the upper reaches of the Tarim River. The soil quality assessment values (SQAV) were visualized using principal component analysis (PCA), and the soil quality grades were classified with a clustering diagram. The sustainable yield indexes (SYI) were calculated to verify the evaluated results. The results show that there are differences, in terms of the physical, chemical and enzymatic properties, between the continuous cropping cotton fields for the different years, and that continuous cropping of cotton has a significant influence on a number of soil properties. Soil quality initially increased, but then decreased gradually with continuous cropping. The soil quality in continuous cropping cotton fields at 8 and 12 years improved, but was degraded for 20 and 30 years. In the early stages, soil fertility increased through fertilization, irrigation and growth, and soil organic matter, nutrients and enzymatic activity subsequently rose, and soil quality improved. Cropped cotton fields at 3 years exhibited the lowest soil quality. Indicator values and the soil quality assessment values reached their maximum at 12 years. With continuous cotton cropping, soil quality gradually dropped in a monoculture pattern over a long period. Organic matter levels declined significantly, along with total N, polyphenol oxidase, invertase and alkaline phosphatase. Soil ecosystems undergo a series of degradation stages, and the soil texture was appeared to be transforming into brown desert soil. The soil quality assessment values decreased from 0.633 to 0.068 between 12 and 30 years. Different land use intensities and cropping patterns would significantly impact the soil quality, and extended cultivation for more than 10 years may also cause a decline in soil quality, to a varying degree, with unreasonable tillage practices. Soil quality values were consistent with sustainable yield indexes, but the latter lagged the former appreciably. Therefore, management practices need to consider increasing soil quality through irrigation, cotton-green manure usage, crop rotation and the combined application of organic and chemical fertilizers. This study could be beneficial for refining a sustainable agricultural development in the oasis. It is recommended that studies into the soil quality of arid lands be focused on defining a Minimum Data Set (MDS), with the aid of multivariate statistical techniques and an analysis of the relationships between different soil factors.