【Objective】Soil fertility is significantly influenced by plough layer thickness. However, it is still not clear how the transformation and fate of fertilizer nitrogen (N) in fluvo-aquic soils would be affected by plough layer thickness. 【Method】In this study, a soil column simulation experiment in the field was conducted throughout three crop cultivations. The experiment was performed in a completely randomized design with six treatments including two plough layer thicknesses (15 and 25 cm) and three soil textures (sandy loam, sandy clay loam and loamy clay). A 15N-labeled tracer technique was used to evaluate the dynamics of fertilizer-derived organic N, fixed NH4+ and mineral N in 0~40 cm soil layer and the fate of fertilizer N in soil-crop systems. 【Result】The transformation of fertilizer N in soil-crop systems was significantly affected by plough layer thickness, and showed the same varying tendency among different textural soils. The residual fertilizer N existed mainly in the form of organic N, which accounted for more than 83% of the total residual fertilizer N and played a pivotal role in the storage and supply of fertilizer N. Increasing plough layer thickness degraded the conversion of fertilizer N to fixed NH4+ pool, while increased the stocks of fertilizer-derived organic N in 0~40 cm soil layer. In the current season after fertilizer N was applied, the average value of fertilizer-derived organic N stock in soils with 25 cm plough layer thickness (PLT-25) was averagely 8.9% higher than that in soils with 15 cm plough layer thickness (PLT-15). The stocks of fertilizer-derived mineral N under PLT-25 treatments were also higher than that under PLT-15 treatments in the current and subsequent crop cultivations; promoting the fertilizer N uptake by crops. The N use efficiency under PLT-25 treatments in the first two crop cultivations was about 8.0% higher than that of PLT-15 treatments, while the current seasonal loss rate and cumulative loss rate of fertilizer N were 12.3% and 9.1% lower, respectively. The stocks of fertilizer-derived organic N in sandy clay loam and loamy clay were significantly (P < 0.05) higher than that in sandy loam, while the trend was the opposite for the stocks of fertilizer-derived fixed NH4+. And the fertilizer-derived mineral N stock was usually to be higher in sandy loam. Overall, the percentage of recovery of applied fertilizer N in crops and soil under sandy loam treatment was significantly (P < 0.05) lower than that in sandy clay loam and loamy clay. Also, the percentage of cumulative loss of fertilizer N in sandy loam was 18.8% and 20.8% higher than that in sandy clay loam and loamy clay, respectively. 【Conclusion】The fluvo-aquic soils with higher sand content have lower fertilizer N storage capacity, restricting the enhancing of N use efficiency. For fluvo-aquic soils with different textures, increasing plough layer thickness could improve the annual N use efficiency and the residual amount of applied fertilizer N in the current season. This, could be released for crop uptake in the subsequent crop cultivation. In typical fluvo-aquic soil areas, increasing the plough layer thickness may be a potential means for regulating the transformation and fate of applied fertilizer N, increasing fertilizer N retention, enhancing the fertilizer N uptake by crops and minimizing fertilizer N loss in soil-crop systems.