Appropriate crop nutrient management synchronizing soil nutrient supply with crop nutrient demand is critical for global food security, soil and agriculture sustainability, and ecological environmental protection. Rational nutrient stewardship should be embodied in application of climate-soil-crop-specific types of fertilizers, at the right rate, right time and right place. However, most of the current N nutrient management practices often fail to take into account the influences of N species preferences of crops, soil N transformation characteristics and climate conditions, thus affecting the effects of the soil N nutrient management practices. Meanwhile, any mismatching of these factors would increase N losses through ammonia volatilization, denitrification, runoff and leaching. Nitrogen transformation is liable to get affected by climatic conditions and responds to plant N uptake characteristics in natural ecosystems. For instance, in subtropical acidic soils, NH₄⁺-N dominated inorganic N pool is mainly a result of low nitrification and relative high nitrate immobilization, which reduces the risk of N loss via leaching or runoff. In contrast, in neutral and alkaline soils in arid and semiarid regions, NO₃^--N is the dominant inorganic N form, as a result of high nitrification and relative low nitrate immobilization and denitrification, which reduces the risk of N loss via ammonia volatilization under high pH condition. Some crops, such as rice, already adapted to low redox potential and tea, originating from acidic soils, prefer NH₄⁺-N, and most crops growing in dryland, like wheat, tobacco and maize, and a variety of vegetables prefer NO₃^--N. Therefore, a closed N cycle with minimal N loss in ecosystem might be achieved through rationalizing N nutrient management, exhibiting that the N available in the soil matches the N of the plant’s preference in form. If the applied NH₄⁺-based fertilizers are always maintained in the form of NH₄⁺ in the soil, “preference” for NH₄⁺ of NH₄⁺ preferring crops can often be translated into higher ¹⁵N recovery by the crops. In contrast, if the N applied doesn’t match the crop's preference in form, availability of the applied N to the crop depends on ability of the soil to transform the applied N into the preferred N in form. Hence, soil N transformation regulating soil N forms plays an important role in optimizing matching degree N sources with plant’s species-specific N preferences. This paper points out that to satisfy crop N preference, it is essential to have N form in fertilizer, soil N transformation characteristics and climate conditions well coupled and only in this case, can N use efficiency be significantly improved, N application rate lower, and loss of active N via emission into the environment be reduced. Therefore, it could be concluded that (1) NH₄⁺- preferring crops perform best in acidic soils, in low nitrification rate, in humid regions and applied with NH₄⁺-based fertilizers as the sole N source; and (2) NO₃^--preferring crops perform best in neutral and alkaline soils, in high nitrification rate, in arid and semiarid regions, and applied with NO₃^--based fertilizer as the main N source. So, these relationships should be taken into account when new N fertilizer management strategies are developed and new species of crops are introduced (e.g. application of nitrification inhibitors to rice paddy fields (prefer NH₄⁺) can increase N uptake and yield). It is expected that this study would provide a scientific basis for development of knowledge-based N fertilizer management practices for a certain crop, soil and climate system. To establish critical values to evaluate coupling degree of the N sources, soil N transformation characteristics, crop N preference and climate conditions, further studies should be conducted.