Abstract: 【Objective】 As important carbon sources and sinks in terrestrial ecosystems, the accumulation process of paddy soil organic matter (SOM) is relatively well understood. However, changes in the molecular composition of SOM within soil aggregates and the mechanisms underlying SOM accumulation remain unclear.【Method】This investigation employed a paddy soil chronosequence in Cixi, utilizing Fourier Transform Infrared Spectroscopy (FTIR) and three-dimensional excitation-emission matrix fluorescence spectroscopy (3D-EEM). These methods were implemented to elucidate the variation patterns of SOM molecular components across different aggregate sizes and their contributions to SOM sequestration processes within the paddy chronosequence.【Result】Our findings revealed distinct temporal patterns in soil organic carbon (SOC) dynamics. Both macroaggregates (>250 μm) and microaggregates (<250 μm) exhibited rapid SOC accumulation within the initial century, followed by a gradual stabilization. Aliphatic SOM components demonstrated a substantial decrease from 12%-13% to 1% within the first 100 years of rice cultivation, while aromatic SOM components showed a progressive increase from 16%-17% to 30%-38%. In dissolved organic matter (DOM) fractions, tryptophan-like DOM increased from 16%-17% to 33%, whereas fulvic acid and humic acid components decreased from 41%-42% to 36%-37% and 31%, respectively, subsequently maintaining relative stability. The fluorescence index (FI) and autochthonous index (BIX) of DOM displayed an initial increase followed by a decrease, while the humification index (HIX) showed the opposite trend. These observations suggest an initial period of microbial activity characterized by high metabolic substance content, followed by microbial community stabilization and continuous production of complex humic substances during prolonged rice cultivation.【Conclusion】Despite relatively minor differences in SOC molecular components across various aggregate sizes under extended rice cultivation, our results substantiate that SOC accumulation in paddy fields is influenced not only by chemical adsorption and physical protection within soil aggregates but also significantly by microbial transformations. These findings contribute to a comprehensive understanding of SOC accumulation mechanisms in paddy soils and provide valuable insights for enhancing soil fertility sustainability.