According to the theory of set pair analysis and trend regression analysis, the paper selected the indexes such as total hardness, total dissolved solids, sulfate and fluoride to analyze the water quality status and variation trend in desert area of Xinjiang. The results show that the water quality of majority water wells are class Ⅲ, few of them are class V. Through linear regression analysis it is found that in recent 10 years the total hardness, total dissolved solids and fluoride content tend to increase, and the remaining indicators changes little. Taking the local hydrogeological conditions into account, it is believed that the factors which influence groundwater environment are over exploitation of groundwater and evaporation and oxidation reduction reaction.