Abstract: Integration of soil and water resources conservation and maintaining of stable high yield is the main challenge during the land cultivation in Yili, Xinjiang Autonomous region. In this study, 2 years of organic rice production experiment was undertaken in Yili river basin for the analysis of impact of organic and chemical fertilizers on paddy yield and its components, soil nutrients balance, nutrient utilization efficiency and nitrogen risks. The results indicated that under organic farming, rice yield increased by applying of cattle and sheep manure which impacted on the number of grains per rice ear and thousand seed weight, while conventional farming contributed by tillering and the number of grains per rice ear. The best proportion animal manure treatment increased soil organic matter but not on soil total nitrogen. The N, P and K balances for organic rice treatments were in 106-678 kg/hm2, 26-166 kg/hm2 and 79.5- 627.3 kg/hm2, respectively. Nitrogen apparent recovery and agronomic efficiency of organic rice production for lowest and highest animal manure treatments were 17.1%, 10.6 kg/kg and 8.7%, 4.9 kg/kg respectively. The highest proportion animal manure treatment could achieve 80% of rice yield for conventional rice production. higher proportion animal manure increased rice yield but also had low nutrient utilization efficiency and potential non-point source pollution of nitrogen in the current newly cultivated region. The study can provide technical support for sustainable usage of water and land resources during Yili reclamation area comprehensive development process.