Crop residue returning to field inputs considerable nitrogen (N) into soils, which greatly influences the function and sustainability of the agricultural system. However, little is known about the transformation and physical stabilization of maize residue-derived N in soil matrix in response to changing N availability. To explore the distinct regulation of organo-mineral complexes on maize residue N translocation, a 38-week microcosm incubation was carried out amended with ¹⁵N-labeled maize residue in a Mollisols sampled from Gonghzuling, Northeast of China. Unlabeled inorganic N was added at different levels (0, 60.3 mg N kg⁻¹ soil (low level), 167 mg N kg⁻¹ soil (medium level), and 702 mg N kg⁻¹ soil (high level)). ¹⁵N enrichment in bulk soil and the separated particle size fractions were determined periodically in the bulk soils and the subsamples were analyzed. At the early stage of the incubation, the maize residue N concentration declined significantly in the sand fraction and increased in the silt and clay fractions. Temporally, the ¹⁵N enrichment in the silt fraction changed slightly after 4 weeks but that in the clay fraction increased continuously until the 18th week. These results indicated that the decomposing process controlled maize residue N translocation hierarchically from coarser into finer fractions. From the aspect of functional differentiation, the pass-in of the maize residue N into the silt fraction was apt to be balanced by the pass-out, while the absorption of clay particles was essential for the stabilization of the decomposed maize residue N. The inorganic N level critically controlled both the decomposition and translocation of maize residue in soil. High and medium inorganic N addition facilitated maize residue N decomposition compared to the low-level N addition. Furthermore, medium N availability is more favorable for maize residue N transportation and stabilization in the clay fraction. Comparatively, high-level inorganic N supply could possibly impede the interaction of maize residue N and clay minerals due to the competition of ammonium sorption/fixation on the active site of clay. This research highlighted the functional coupling of organic–inorganic N during soil N accumulation and stabilization, and such findings could present a theoretical perspective on optimal management of crop residue resources and chemical fertilizers in field practices.