Aiming to analyze crop nitrogen uptake, nitrogen utilize efficiency, soil ammonia-oxidizing mushroom and nitrogen concentration in surface water based on a fertilization field experiment to select an environmentally friendly nitrogen application practice in the area along Yangtze River. Five treatments were designed, including non fertilization (CK), traditional fertilization (NPK, 225kg/hm2), equivalent nitrogen (CRF1), reducing 15% nitrogen (CRF2), and reducing 25% nitrogen (CRF3) by controlled release mixing fertilizer. Results showed that there was no significant difference in the rice yield except for CRF2 among NPK, CRF1 and CRF2 treatments. Compared with NPK treatment, the values of crop nitrogen uptake, nitrogen utilize efficiency and direct economic benefit under CRF2 treatment were increased by 7.4%, 10.7%, 43.4% and 27.2%, respectively. Ammonia-oxidizing archaea (AOA) accounted for between 73.5% and 88.4% was the dominate mushroom in the paddy soil. Compared with NPK treatment, the ratios of AOA accounted for ammonia-oxidizing mushroom under CRF1, CRF2 and CRF3 treatments were significantly (p<0.05) increased by 13.6%, 9.9% and 6.0%, respectively. It was indicated that the intensity of soil ammonia-oxidizing process could be reduced. Compared with NPK treatment, the concentrations of total, dissolved and particulate nitrogen in surface water under CRF2 treatment were significantly decreased by 13.2%, 10.6% and 33.7%, respectively. The corresponding values under CRF3 treatment were 24.9%, 22.9% and 40.6%, respectively. In conclusion, our findings indicated that controlled release mixing fertilizer application, especially for reducing 15% nitrogen (190kg/hm2), was a prefer nitrogen management practice for maintaining rice yield, decreasing intensity of soil ammonia-oxidizing process, improving nitrogen efficiency and reducing the risk of agricultural non-point nitrogen pollution. Therefore, the practice should be recommended in the single cropping rice region down the Yangtze River.