The qualitative and quantitative characteristics of soil organic carbon (SOC) and related humic acids (HAs) extracted from the soils of field plots were investigated after 8 years of annual paddy (Oryza sativa L.) and upland maize (Zea mays L.) rotation with various fertilizations. Seven fertilization treatments were selected: Ck (no inputs); Chem (chemical fertilizer of NPK); Comp (swine compost); Comp + 33% of Chem N rate; Comp + 67% of Chem N rate; GM (legume green manure) + 33% of Chem N rate; and peat + 33% of Chem N rate. Organic and inorganic nitrogen inputs of six treatments were equivalent with respect of nitrogen content, but Comp, GM, and peat treatments were complemented with various amounts of inorganic N. After harvest of the eighth paddy crop, surface soil samples collected from the plots were subjected to soil characterizations and extraction of humic substances, which were used for chemical, spectroscopic (FTIR, 13C NMR, ESR, X-ray diffractometry), delta13C, and 14C dating analyses. The yields of HAs extracted from the seven treatments were significantly different. Treatment containing persistent organic compound such as the peat + 33% N treatment increased the humification process in topsoils and produced higher yield of HA. Spectroscopic analyses revealed that fertilization treatments changed the functional groups, alkyl C, crystalline characteristics, and delta13C ratios of HAs and turnover rate of SOC considerably. The SOC of the peat + 33% N treatment had the highest mean residence time of 3100 years. Various fertilizer treatments are correlated with turnover rate of SOC and related HAs, which are associated with concerned carbon sequestration as well as mitigation of CO2 emission in the soil environment.