The accumulation and availability of soil organic nitrogen (N), especially amino acid N, is highly important for N retention in the soil and N supply for crop growth. However, it remains obscure how the conversion of fertilizer N to both soil organic N and amino acid N is affected by management practices such as fertilization and residue amendment. In present study, we conducted an outdoor N-15 labeling pot experiment in Mollisols of Northeast China, where plants were consecutively cropped after each of three cultivations (spring wheat-buckwheat-spring wheat). We aimed to evaluate the effects of maize straw applications on the dynamics of organic N and amino acid N derived from fertilizer N. Six treatments were set: no N fertilization (CK), application of only maize straw (M), low N levels (N-1), N-1 plus maize straw (N-1 + M), high N levels (N-2), and N-2 plus maize straw (N-2 + M). The results showed that organic N and amino acid N dominated the available N derived from fertilizer N, but their contents decreased significantly as crop cultivation continued. Compared with N-2, N-2 M, which involved the application of maize straw, significantly increased the content of organic N derived from fertilizer N by an average of 20.1% during the first crop cultivation. Compared with N-1 and N-2, N-1 M and N-2 + M promoted the content of fertilizer-derived amino acid N by an average of 12.5% across five sampling dates. During the first crop cultivation, straw amendment also significantly increased both plant uptake and soil residues of fertilizer N in N-1 + M and N-2 + M. Our results demonstrated that substrate amendments such as crop residues may constitute a practical agricultural management approach for promoting the transformation of fertilizer N to soil organic N, thereby increasing both fertilizer N use efficiency and retention in our study crop-soil systems.