Abstract: Thirteen key indicators of water resources system and agricultural system were selected to form a comprehensive evaluation index system．Entropy method was used to determine weights of indicators, and capacity coupling content in physics was referenced to establish a water resources system and agricultural system coupling coordination model．Based on water resources and agricultural economic development status of Changji Hui Autonomous Prefecture（referred to as Changji Prefecture）in Xinjiang Uygur Autonomous Region, comprehensive coordination degree between water resources system and agricultural system was divided into three stages and eight types．Evaluation results indicated that, in the past 21 years, water resources and agricultural development in Changji Prefecture have mutually influenced and constrained each other, and rapid development of agriculture has led to a significant consumption of water resources．Due to constraints of water resources, utility of agricultural development has shown a decreasing trend, and coupling and coordination between water resources system and agricultural system has deteriorated to a state of imminent imbalance and decline．After 2015, Changji Prefecture strengthened implementation of strictest water resource management system, strictly controlled "three red lines", and orderly promoted a series of policy measures such as water conservation and efficiency improvement, water reduction and land use reduction, and cleaning actions．Ecological environment of water resources has been improved, and degree of coupling and coordination has been enhanced．In the future, Changji Prefecture should improve water right distribution system, promote efficient agricultural water-saving technology, reduce irrigation area, carry out bioengineering construction and reduce mining output of groundwater, promote advantages and eliminate disadvantages, reform the old and innovate the new, give full play to maximum benefits of water resources, and achieve sustainable development of regional agriculture．