Objectives Dissolved organic matter (DOM) is an important parameter to characterize the dynamics of soil organic carbon, and soil aggregate particle size is an important factor for the sequestration and protection of soil organic carbon (SOC). Understanding the distribution characteristics of DOM in aggregates of different grain sizes is of great significance for revealing the mechanism of soil carbon cycling in farmland under management measures.

Methods A long-term experiment started since 1984, three typical fertilization methods (control CK, inorganic NP, organic and inorganic combined application of NPM) were selected, and four aggregate particle fractions (>250 μm, 125−250 μm, 63−125 μm and <63 μm) were screened, the DOM content in the aggregates of each particle size was determined and the DOM components and spectral characteristics were characterized by three-dimensional fluorescence spectroscopy (3D-EEM) and ultraviolet-visible absorption spectroscopy (UV-Vis).

Results Fertilization significantly increased the soil DOC content in >250 µm and 125−250 µm aggregates, with increases of 42.0% and 44.9% under NP treatment, and increases of 25.0% and 20.0% under NPM treatment, respectively. At the same time, NPM treatment significantly increased the SUVA₂₅₄ values of each particle size aggregate, and the SUVA₂₅₄ values of > 250 μm, 125−250 μm, 63−125 μm and <63 μm aggregates increased by 43.6%, 86.8%, 121.5% and 144.9%, respectively, indicating that the aromatic properties of DOM in small particle size (63−125 μm and <63 μm) aggregates were stronger, which was conducive to soil more effective adsorption and fixation of organic carbon. The humification index (HIX) increased most significantly under NP treatment, with the >250 µm, 125−250 µm, and 63−125 µm aggregates increasing by 93.08%, 99.18%, and 47.10%, respectively, while the HIX of <63 µm aggregates did not show a significant increase. This indicates that fertilization enhances the humification of DOM in soil aggregates, promotes organic carbon stabilization, increases soil carbon storage, and simultaneously improves soil structure and fertility, providing better conditions for crop growth. NP treatment significantly reduced the BIX value of each aggregate by 48.83%, 25.00%, 16.49% and 8.90%, respectively, while NPM had no significant effect, indicating that long-term application of chemical fertilizer inhibited microbial activity and slowed down soil organic carbon decomposition. In addition, the DOM content of soluble microbial metabolites and tyrosine-like components in the aggregates after fertilization was the highest, and the content of fulvic-like components was the lowest.

Conclusions Long-term combined application of nitrogen and phosphorus organic fertilizers can increase the content of soluble organic matter in soil aggregates, enhance the aromaticity and humification coefficient of aggregate 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.