To elucidate compositional succession and transformation mechanisms of dissolved organic matter (DOM) following Chinese milk vetch (Astragalus sinicus) incorporation under nutrient gradients, we established a fertilizer-input gradient in a red-soil paddy field and collected soils at multiple time points after green-manure incorporation. Soil physicochemical analyses showed that increasing fertilizer inputs elevated total nitrogen (TN) and significantly enriched total phosphorus (TP) and available phosphorus (AP), accompanied by a slight decline in pH. Fluorescence excitation–emission matrices (3DEEMs) coupled with parallel factor analysis (PARAFAC) were used to resolve DOM fluorescent components, while the fluorescence indices (FI), biological index (BIX) and humification index (HIX) were calculated to evaluate DOM source characteristics, humification, and bioavailability. PARAFAC identified five components, among which humic-like components (C1, C2, and C5) were consistently enriched under higher fertilizer treatments, whereas the protein-like component C4 declined, indicating a shift of DOM from more labile fractions toward more stable humic-like structures. Consistently, FI and BIX decreased and HIX increased with fertilizer input, and a pronounced inflection occurred at the second sampling period after Chinese milk vetch incorporation, indicating that DOM entered a humification accumulation stage after rapid transformation during the early incorporation period. Overall, increased chemical fertilizer application promoted DOM stabilization through nutrient enrichment and the accompanying acidification background. These findings suggest that fertilizer application intensity should be optimized in Chinese milk vetch incorporation systems to balance carbon retention and the maintenance of soil processes.