Background: Inorganic fertilizer is one of the most important anthropogenic inputs which influences soil nutrient turnover in agricultural ecosystems. However, as the key process involved in the maintenance, transformation and stability of soil nitrogen (N), the incorporation and allocation of fertilizer N between different soil organic N (SON) fractions in a growing season remains largely unknown. Methods: In this study, a field experiment was conducted in triplicate of micro-plots and a total of 200 kg N ha −1 ( 15 N-labeled (NH 4) 2SO 4, 98 atom %) was applied as a basal dressing and two top dressings, at jointing and filling stages, respectively, to a maize crop during one growing season. The distribution and seasonal dynamics of fertilizer N in different SON fractions (i.e., amino acids, amino sugars, hydrolyzable ammonium N and acid insoluble-N) were measured by liquid/gas chromatography–mass spectrometry (LC/GC-MS) and element analysis-combustion-isotope ratio mass spectrometry (EA-C-IRMS) techniques. Path analysis was used to evaluate the transformation processes between organic N fractions derived from fertilizer and N supply strategy in soil-plant system. Results: The accumulation of fertilizer-derived N in different organic fractions was season-specific. At jointing stage, preferential enrichment of 15 N was found in soil amino acids plus amino sugars, indicating the active biological immobilization of basal dressing fertilizer N. Nevertheless, there is still a small proportion of fertilizer N stabilized in the acid insoluble fraction. The accumulation of the residual fertilizer N in hydrolyzable ammonium N reached a maximum at filling stage and then declined significantly, implying the rapid release of the fertilizer N remained in mineral forms. The contents of amino acids changed slightly, but they played a very important role in mediating SON transformation. Conclusion: The hydrolyzable ammonium N was a temporary pool for rapid fertilizer N retention and simultaneously was apt to release N for crop uptake in the current season. In contrast, the amino acids could serve as a transitional pool of available N in the soil-crop system, while the acid insoluble fraction was as a stable pool of fertilizer N. Importantly, there is an interim shift among different pools to maintain soil N turnover; hence N in the amino acid fraction mediates N supply and the depolymerization of SON constituents controls the proceeding of fertilizer N cycling in the soil-plant system. [ABSTRACT FROM AUTHOR]