Objectives Dissolved organic matter (DOM) is an important parameter to characterize the dynamics of soil organic carbon, and soil aggregate size plays a critical role in the sequestration and protection of soil organic carbon (SOC). This study elucidates the evolutionary characteristics of dissolved organic matter (DOM) composition across soil aggregate size fractions under different fertilization regimes, based on DOM content, UV–visible spectral parameters, and variations in fluorescence component characteristics.

Methods A long-term experiment was established in 1984, three typical fertilization treatments were examined: no fertilization (CK), inorganic fertilizer (NP), and combined organic and inorganic fertilization (NPM). Soil aggregates were separated into four size fractions (>250, 125−250, 63−125 and <63 μm). DOC content in each aggregate fraction were determined, and DOM composition and spectral characteristics were characterized using three-dimensional fluorescence spectroscopy (3D-EEM) and ultraviolet-visible absorption spectroscopy (UV-Vis).

Results Fertilization significantly increased DOC contents in the >250 and 125−250 µm aggregate fractions. Under NP treatment, DOC increased by 42.0% and 44.9%, respectively, while under the NPM treatment, increases of 25.0% and 20.0% were observed. At the same time, the NPM treatment significantly increased the SUVA₂₅₄ values across all aggregate size fractions, with increases of 43.6%, 86.8%, 121.5% and 144.9% in the > 250, 125−250, 63−125 and <63 μm fractions, respectively. These results indicate that DOM in smaller aggregates (63−125 μm and <63 μm) exhibited stronger aromaticity, which is more conducive to effective adsorption and stabilization of organic carbon. The humification index (HIX) increased most significantly under the NP treatment, with increases of 93.1%, 99.2%, and 47.1% in the >250, 125−250, and 63−125 µm fractions, respectively, whereas on significant change was observed in the <63 µm frcation. This indicates that fertilization enhanced the humification degree of DOM in soil aggregates, promoted organic carbon stabilization, increased soil carbon storage, and simultaneously improved soil structure and fertility, providing better conditions for crop growth. The NP treatment significantly reduced the BIX value in >250, 125−250, 63−125, <63 μm aggregate fractions by 48.83%, 25.00%, 16.49% and 8.90%, respectively, while the NPM treatment showed no significant effect. This indicates that long-term application of chemical fertilizer inhibited microbial activity and slowed down soil organic carbon turnover. In addition, DOM in soil aggregates was dominated by dissolved microbial metabolites and tyrosine-like components after fertilization, while fulvic-like components accounted for the lowest proportion.

Conclusions Long-term combined application of nitrogen and phosphorus organic fertilizers can increase dissolved organic carbon content in soil aggregates, and enhance the aromaticity and humification coefficient of aggregate-associated organic matter, thereby optimizing soil structure and improving soil fertility and ecological function. However, applying chemical fertilizers alone is not conducive to the decomposition of organic carbon. Therefore, in rainfed agricultural areas, the management practice of combining nitrogen and phosphorus organic fertilizers is recommended as an effective strategy to promote the stability of soil organic matter and achieve sustainable agricultural development.