Objectives We investigated the rice yield and soil nutrient and pH variations caused by nitrogen application rates under no-tillage cultivation practice in a fish-rice integrated farming system, so as to provide a theoretical basis for long-term and reasonable fertilizer management under the system.

Methods A localized field experiment was carried out for five years in a winter logging-water field in Southeast of Sichuan Province from 2018 to 2022. No-tillage cultivation practice was used, and two hybrid rice cultivars Rongyou 1015 and Nei 6you 103 were used as test materials. Four N fertilizer treatments were 0, 45, 90 and 135 kg/hm² (denoted as N₀, N₄₅, N₉₀, and N₁₃₅), representing low, meddle and high N rate, except the N₀. At rice harvesting stage of each year, the grain yield, yield components, and nitrogen content in different part of hybrid rice were analyzed. The soil total and available N, P and K content, and the pH in 0−20 cm layer were determined.

Results Experimental years and N rates significantly affected grain yield and yield components of hybrid rice in the rice-fish integrated farming system. During the five years, the grain yield was positively correlated with N rate (F_year=7.95^**−63.44^**, F_{N rate}=3.95^*−282.99^**). Compared with N₄₅, N₉₀ and N₁₃₅ treatment increased grain yield by 6.37%−26.53% and 9.11%−25.11%, respectively, due to the higher panicle number per unit area and spikelet per panicle. And N₉₀ was also recorded similar or even higher grain yield, compared with N₁₃₅. Stepwise regression analysis showed that the yield components were positively correlated with grain yield, and the path analysis showed that panicle number and spikelets per panicle had the highest direct contribution (0.8754 and 0.4987, respectively) and total contribution (0.6364 and 0.3598, respectively) to grain yield. In the fish-rice integrated farming, soil pH significantly decreased with the elongation of experimental years (r=−0.9823^** −0.9385^**), while soil organic matter, total and available P and K kept increased (r=0.7128^**−0.9932^**). The soil total and alkali hydrolyzed N (AN) significantly decreased with the increase of experimental years under N₀ and N₄₅, but significantly increased under N₉₀ and N₁₃₅. There was a linear relationship (P<0.01) between grain yield and soil nutrient content under rice-fish integrated farming system, and improving the supplying capacity of soil phosphorus and potassium was an important approach to obtain high rice grain yield.

Conclusions The optimal N application rate for hybrid rice is 90 kg/hm² under rice-fish co-culture system, due to the higher panicle number per unit area and spikelet number per panicle of hybrid rice. Continuous application of medium and high nitrogen rate could increase soil organic matter, total and available nitrogen, phosphorus, and potassium, and the organic matter and nutrient contents tend to become higher with the extension of rice-fish co-culture years, while the soil pH is on the opposite. So nitrogen application rate should be controlled to relatively low level in the rice-fish co-culture system of southeast of Sichuan Province.