【Objective】The molecular composition of soil organic matter (SOM) is central to understanding carbon cycling in agroecosystems. However, how the SOM molecular composition evolves under long-term different fertilization regimes remains poorly understood. This study aimed to elucidate the regulatory mechanisms of long-term fertilization on SOM molecular composition in red soil paddy fields.【Method】Based on a long-term field experiment, four treatments were selected: no fertilizer (CK), organic matter recycling (C), chemical NPK fertilizers (NPK), and chemical NPK fertilizers plus organic matter recycling (NPKC). Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) was employed to analyze the molecular composition of SOM.【Result】(1) All fertilization treatments significantly increased soil organic carbon (SOC) and total nitrogen (TN) contents, while the NPK treatment specifically enhanced dissolved organic carbon (DOC) and dissolved organic nitrogen (DON) contents. (2) CHO-type compounds dominated the SOM composition, accounting for 64.0% of all identified molecular formulas. (3) Compared with CK, fertilization, especially NPKC, significantly increased the relative abundance of lipid-like compounds, whereas CK enriched more plant-derived lignin-like compounds. (4) Different fertilization treatments altered the molecular classes of SOM. Specifically, the molecular composition of lipids, tannins, lignins, and carbohydrates differed significantly among fertilization treatments, whereas the responses of condensed aromatics and unsaturated hydrocarbons to fertilization were not significant.【Conclusion】This study demonstrates that long-term fertilization reshapes the molecular composition of SOM in red soil paddy fields primarily by regulating key components, including carbohydrates, tannins, lipids. This and lignins, provides direct molecular evidence for fertilization-induced alterations in soil organic matter composition.