To evaluate the soil quality in the main cotton growing regions of Xinjiang, 11 soil quality indices were measured in representative locations: Hami, Bole, Changji, Shihezi, Aksu, Kashgar and Kuitun. The indices included soil pH, salt, organic matter, total N, available P and available K for soil physicochemical properties, and Cr, Cu, Zn, As, and Pb for soil heavy metal pollution. Based on these indices, a comprehensive soil quality index (SQI) was developed to analyze the soil quality in the cotton fields of Xinjiang. The results showed that the soils in Xinjiang's cotton fields were alkaline, with an average pH of 7.87. The soils were mildly saline, with an average salt content of 3.44 g·kg-1. Soil organic matter and total N concentrations were generally low, whereas available P and available K concentrations were relatively high. Soil available P concentrations were significantly higher than that of the second national soil survey, whereas soil pH, salt content, organic matter, and total N were less. Soil available K was greater in some regions but lower in others compared with the second national soil survey. The average heavy metal concentrations were as follows: Cr, 45.88 mg·kg-1; Cu, 40.66 mg·kg-1; Zn, 68.30 mg·kg-1; As, 12.88 mg·kg-1; and Pb, 16.68 mg·kg-1. These values were all below the national standards. However, the Cu, Zn, and As concentrations were greater than the background values in Xinjiang, indicating the accumulation of those elements in the soils. When the Nemerow comprehensive pollution index (PN) of heavy metals was less than 0.5, the comprehensive soil quality improved as the soil physicochemical properties improved. Soil organic matter, total N, Cu, Zn, As and Pb were the main variables affecting soil quality in the main cotton cropping regions of Xinjiang. The cotton growing areas in Xinjiang generally had medium soil quality. Changji and Kuitun had the highest SQI (0.52) whereas Aksu had the lowest value (0.31). Soil quality was generally highest in northern Xinjiang, followed by western area, and then southern area.