Background: Minimum tillage (MT) and organic farming (OF) are increasingly conducted in agricultural managements from the interest of optimizing soil conditions and developing sustainable agriculture. Our understanding of their effects on water-extractable organic matter (WEOM) is still insufficient. Methods: To study the effects of MT and OF on WEOM, we analyzed soil materials sampled at two depths (0–8-cm-upper soil and 12–25-cm-deeper soil) from long-term field experiments using different farming and tillage methods. The content, composition, and quality of WEOM were examined. Results: The results showed organic farming significantly decreased water-extractable organic carbon and nitrogen, but had positive effect on WEOM humic-like components revealed by parallel factor analysis with excitation–emission matrix, soil organic carbon (SOC), total nitrogen (TN), as well as SOC/TN. In addition, organic farming increased the aromaticity and condensation of WEOM as indicated by specific UV absorption and humification index. MT had no effect on WEOM both quantitatively and qualitatively but significantly decreased SOC and TN of the whole investigated soil profile. The depth effect was significant with strong stratification of WEOM, WEOM components as well as SOC and total N in upper soil. Moreover, the WEOM spectroscopic quality showed sharp differences between the upper and deeper soils. Conclusions: The results indicated that in the combined presence both tillage management and farming management, farming management imposed more influence on WEOM than tillage, and organic farming may facilitate the transformation of WEOM and lead to formation of WEOM with high stability. MT significantly changed the distribution of SOC and WEOM in soil, profile but did not increase the contents of SOC and WEOM in the site of the present study. However, the presence of larger pool of WEOM in MT + OF treatment at upper soil is likely to fuel possibly greater microbial activity and more rapid nutrient cycling in soil which can be favorable practice with potential in improving soil conditions in view of developing a sustainable ecosystem in the studied site[Figure not available: see fulltext.].