Objective The high chemical nitrogen (N) fertilizer input in cropland soils of China has caused a large accumulation of residual fertilizer N in the soil in the current-season. This soil-residual fertilizer N can either be absorbed by subsequent season crops or lost to the environment through gaseous and hydrological pathways. The rice-wheat rotation is a dominant vital cropping system in the middle and lower reaches of the Yangtze River agricultural region in China. However, the residual effects and fate of the soil-residual fertilizer N in this cropping system remain unclear.Method In this study, a ¹⁵N tracer long-term in-situ experiment was used to continuously monitor the fate and the residual effect of soil-residual fertilizer N in the following 17 years under non-fertilizer N application in a rice-wheat cropping system. The experiment had two N fertilizer treatments, with 100 (N100) and 250 (N250) kg·hm^–2 of labelled urea (30 atom%) applied in the first wheat season, and no N fertilizer was added in the subsequent 17 years of the rice-wheat rotation.Result The results suggested that 34.5%-37.9% of the applied fertilizer N was taken up by the first wheat crop, and then the amount of residual N uptake by the rice and wheat decreased exponentially in the following rice-wheat rotation years. Over the following 17 years, 12.2%-15.8% of the applied fertilizer N was taken up by the subsequent crops (9.2%-11.8% for rice and 3.3%-4.0% for wheat), leading to the accumulative crop N recovery of 50.1%-50.3%, which was significantly higher than the in-season N use efficiency. We found that 22.9%-33.5% of the applied fertilizer N remained in the 0-20 cm soil after in-season wheat was harvested, which was then gradually decreased to 7.8%-9.8% after 17 years, but still accounted for 73.5%-78.5% of the total residual N in the 0-100 cm soil layer (9.9%-13.4%). The cumulative total loss of fertilizer N over the observation period estimated from the isotope mass balance was 36.3%-39.9%, which was close to the total loss of fertilizer N of 32.0%-39.2% calculated based on the N fertilizer use efficiency and the residual rate of 0-20 cm soil in the current season. The ¹⁵N abundance of crop grain, straw and soil all decayed exponentially with time during the observation period, which predicted that it would still take 28-37 years for the crop to decrease to the natural ¹⁵N abundance background value without N application.Conclusion Overall, fertilizer N losses in the rice-wheat cropping system mainly occurred in the current-season, and the residual effects of fertilizer N in soil lasted for a long time, but a negligible amount of this residual N can be lost to the environment. The keyways to optimal N fertilizer management in rice-wheat rotation are effectively reducing in-season fertilizer N losses and better utilizing soil-residual fertilizer N.