Long-term fertilization in loessial soil region on the Loess Plateau in Northwest China significantly affects nitrogen fertilizer use efficiency for wheat, rape, and flax. Combining nitrogen with phosphorus and potassium (NPK) resulted in the highest nitrogen fertilizer use efficiency for wheat and rape. Manure combined with nitrogen (MN) also increased efficiency compared to nitrogen alone. The relationship between annual nitrogen fertilizer use efficiency and crop yield was positive, while the relationship with accumulated nitrogen fertilizer use efficiency was not significant. This suggests that annual nitrogen fertilizer use efficiency is a better indicator of fertilizer effectiveness under specific soil and crop conditions.