Application of nitrogen fertilizers in agricultural systems is one of the most important factors influencing the global nitrogen cycle. Nitrogen fertilizers can improve crop production, but also have much influence on ecological environment. Nitrogen fertilizers in ammonium form (NH₄⁺) is easily transferred into nitrate form (NO₃^-) in dry land by nitrification. However, only a small portion of the formed NO₃^- can be taken up by plants, while a large amount will be leached or released into the air through denitrification, which results in severe nitrogen loss. In nature some plants can excrete through their roots some compounds that have the function of inhibiting nitrification and thus can be characterized as biological nitrification inhibitor (BNI), which may significantly improve nitrogen use efficiency in soil. This review illustrates the origin, excretion and regulation of the substances, mechanisms of their function and potential of their application, and also discusses prospects of their application to high efficiency management of nitrogen in agricultural systems.