Soil dissolved organic carbon (DOC) plays a key role in fundamental biogeochemical processes; however, the influences of different types of fertilization on the chemical composition and properties of DOC molecules in soils are poorly understood. In this study, DOC samples were extracted from gray desert soils treated with five fertilization treatments 1) chemical nitrogen, phosphorus and potassium fertilizers; 2) pig and cattle manure; 3) 50% nitrogen from manure and 50% nitrogen from chemical fertilizer; 4) total chemical fertilizers and total manure; and 5) no fertilization (control). Data were compared by a combination of Fourier-transform infrared spectroscopy, 13C nuclear magnetic resonance, and statistical analyses. Results showed that manure application increased the aliphatic carbon and decreased the aromatic carbon levels, implying manure application promotes the transformation of labile carbon to stable carbon structures. Redundancy analysis indicated that available nutrients and available forms of magnesium were positively associated with the labile carbon groups, and the available forms of calcium were positively associated with the stable carbon groups. These results demonstrated that the availability of soil nutrients and minerals are influential factors on DOC turnover. Moreover, our results showed that fertilization method had negative direct effects on DOC transformation and positive indirect effects on DOC turnover via soil physicochemical factors, and various forms of mineral ions were the strongest explanatory factors of DOC variation. These findings indicated that soil physicochemical factors play an important role as mediators in the influence of fertilization practices on the chemical composition of DOC and turnover of carbon-containing functional groups in DOC.