Finding field management techniques that increase crop output while protecting soil sustainability is essential for maintaining a long-term food supply in a changing environment. However, comprehensive evaluation of the effects of nitrogen (N) reduction combined with organic fertilizer on grain yield, N use efficiency (NUE), water use efficiency (WUE), and soil organic carbon (SOC) and total N (TN) contents of winter wheat–summer maize double cropping systems in drought-prone areas remains limited. Therefore, a 3-year field experiment (2018–2021) was conducted in a winter wheat–summer maize double cropping system with five treatments: no N fertilizer (CK), conventional farmer fertilization (CF), recommended fertilization (R), organic N substitution of 20% of the recommended synthetic N (R₂₀), and organic N substitution of 40% of the recommended synthetic N (R₄₀). When results were averaged from 2018 to 2021, R₂₀ had the highest annual grain yield, which increased by 42.15%, 7.69%, 7.58%, and 12.50% compared with CK, CF, R, and R₄₀, respectively. Compared with CF, R₂₀ increased winter wheat and summer maize NAE, NPFP, NUE, and WUE. In addition, the soil organic carbon content of R₂₀ and R₄₀ treatment increased with the increase in years. In conclusion, R₂₀ was considered ideal for improving crop yield, promoting soil fertility, and increasing the fertilizer utilization rate in a semiarid winter wheat–summer maize rotation.