In order to study the relationship between the composition and structure of dissolved organic matter (DOM) and methane (CH₄) emissions in the paddy soil with Chinese milk vetch returning under different water managements (flooding after a short time delay), we set an incubation experiment, with no green manure and no tillage (DW-0) as control, different water management treatments (immediately flooding, flooding after 5 and 10 days) were set up, three-dimensional fluorescence spectroscopy (3DEEM) and parallel factor analysis (PARAFAC) were used to assess the effects of soil DOM composition and the effect of fluorescence spectra on CH₄ emissions. The results showed that both DOM content and cumulative CH₄ emissions significantly decreased under G+DW-5 treatment, and both DOM content and cumulative CH₄ emissions increased with the extension of dry tillage time. Three fluorescence components, including fulvic-like (C1), humic-like (C2), and protein-like (C3), were obtained by the 3DEEM-PARAFAC method. There were significant differences in the fluorescence components of soil DOM under different water management practices. The highest content of humus-like components (C1+C2) was found in soil DOM under the G+DW-5 treatment, which reached 79.88%, and the restricted principal component analysis indicated that soil DOM components were significantly different under different water management. The DOM Humification Index (HIX) of G+DW-5 was 5.11, significantly higher than other treatments. The correlation analysis showed that CH⁴ emissions were negatively correlated with the C1 and HIX index but positively correlated with the C2 and BIX index; the results showed that flooding after a short time delay could reduce CH₄ emissions by increasing the content of C1 and the level of soil DOM humification. Overall, the composition and structure of DOM in the paddy soil under different water managements are closely related to CH₄ emissions, which could provide a scientific basis for reducing CH₄ emissions from paddy soil.