Organic farming and agroforestry both have the potential to develop sustainable and environmental-friendly agroecosystems and to sequester more soil organic C (SOC). In a long-term field trial, we evaluated the effect of 21-year organic farming and 4-year agroforestry (Robinia and Poplar-based alley cropping system) on water extractable organic matter (WEOM). The technique combining excitation emission matrix (EEM) spectra with parallel factor analysis (PARAFAC) was used to reveal the components of WEOM. In addition, WEOM was characterized by UV absorbance and fluorescence spectra. Organic farming generally increased SOC and total N contents but decreased the WEOM content as well as the WEOM components indicated by the maximum fluorescence intensity (Fmax). Specific UV absorbance (SUVA) and humification index (HIX) of WEOM in organic farming implied WEOM in the organic farming had more components with aromatic structure but less humified. Higher fluorescence (FI) and freshness indices (BIX) of WEOM in organic farming system indicated that a higher percentage of WEOM was microbial-derived in the organic than in the integrated farming system. Robinia showed positive effect on SOC and total N contents in comparison with poplar and had stronger effects on the WEOM components, although the WEOM content did not differ between the two tree species. The significant farming × trees interactions on SOC and water extractable organic carbon (WEOC) indicated that the robinia effects were more pronounced in the organic farming system. Thus, the change of SOC was the result of interactive effect of farming and hedgerow trees in an agroforestry system. The low-input organic farming and robinia tended to result in change of quality of WEOM and led to enrichment of substances of high stability in WEOM. From above, the combination of organic farming and robinia trees is an important means for developing sustainable agricultural systems and soil carbon sequestration.