The influences of integrated practices for high yield and high efficiency on nitrogen (N) leaching and runoff under rice-wheat rotation system were studied with field plot experiment in the Taihu Lake Region. It was found that the leaching of total nitrogen (TN) and organic N (DON) declined with the increase of soil depth and the forms of N leaching changed with soil depth. DON in the percolation water in 60 cm depth, which accounting for 40.5%-58.9% of TN, was higher than NO₃^--N and NH₄⁺-N. NO₃^--N in the percolation water in 80 cm was higher than DON and NH₄⁺-N and accounted for 51.7%-54.7% of TN. NH₄⁺-N loss was the main form of N runoff, and accounted for 48.1%-56.4% of TN. However, N losses via runoff were indistinctive, only accounting for 0.3%-0.6% of fertilizer application. The total loss of N leaching and runoff in the high yield an high efficiency treatments were 10.59 and 10.18 kg/hm², which were lower than in the current treatment with a value of 13.41 kg/hm². The rice yield in high yield and high efficiency treatments was 11.14-12.22 t/hm², and the agronomic efficiency reached 11.8-12.5 kg/kg, which were significantly higher than those of the traditional treatment. After harvest, soil TN content increased by 6.8%-8.1% and soil organic matter by 8.6%-9.2% in high yield and high efficiency treatments compared to traditional treatment. In short, high yield and high efficiency practices can increase crop yield and N use efficiency, weaken the migration of N through water to soil and thus is beneficial to both crop yield and environment.