A comprehensive understanding of the transformation, migration and loss pathways of nitrogen (N) fertilizer was pivotal for optimum nutrient management. Three different cultivation practices (conventional cultivation, plastic film mulching and straw retention) and N rates (0, 144 and 180 kg N ha−1) were assigned as the main plots and split plots separately in a split-plot design during 2017–2020. Moreover 15N-labeled urea was used in each microplot to trace the fertilizer N fate. The results showed that the N recovery efficiencies with plastic flm mulching, straw retention and conventional cultivation were 44–46%, 34–37% and 43–44% in the first season. However, it sharply decreased in the next two seasons. The N residual rates in straw retention and plastic film mulching were 21–26% and 20–27% after three wheat seasons, which were higher than that in conventional cultivation. Furthermore, residual nitrate nitrogen was detected in the deep profiles in plastic film mulching and straw retention at the third season. The ammonia volatilization sourced from fertilizer was 3–5 kg ha−1 in the first season and accounted for 2–3% of the total applied N. Overall, plastic film mulching treatment increased fertilizer N utilization by plants and residual fertilizer N in soil, and reduced unidentified fertilizer N. Although, straw retention depressed fertilizer N uptake by plants, it improved the N budget and had the potential to reduce N input. Accordingly, plastic film mulching and straw retention are recommended in dryland wheat cropping systems. However, we should pay attention to the residual plastic pollution in the practice.