【Objective】 Soil organic matter (SOM) plays an important role in maintaining soil productivity, improving soil quality and sequestrating C. Changes in SOM due to management practices are usually difficult to quantify on the background that the soil already has a large relatively stable SOM pool. Therefore, it is recommended to use SOM fractions as early indicators of effects of management practices on soil quality. Meanwhile, understanding changes in different fractions of functional SOM as affected by long-term management practice may help develop reasonable management strategies to optimize productivity and sustainability of the agroecosystem. 【Method】 Based on a 35-year long-term fertilization experiment, effects of fertilization on SOM relative to functional fraction were explored with the recently developed physical-chemical fractionation method. In the present study, six functional SOM fractions were isolated, including non-protected free labile SOM, physically protected SOM, physico-biochemically protected SOM, physico-chemically protected SOM, chemically protected SOM and biochemically protected SOM, and changes in these six fractions of SOM, concerning size of the fraction and total nitrogen (TN) and soil organic carbon (SOC) contents and ratio in the fraction, under the long-term fertilization were analyzed. The long-term fertilization experiment was designed to have four treatments, that is, treatment CK (no fertilization), treatment N (chemical N fertilizer only), treatment NPK (N, P, K fertilizers), and treatment NPKM (chemical N, P, K fertilizers plus organic manure). 【Result】 Results show that long-term application, especially treatment NPKM, significantly increased the percentages of non-protected SOM (cPOM and fPOM) and physically protected SOM (iPOM) and the contents of SOC and TN therein . The SOC and TN content in the non-protected fraction of free SOM was the highest in Treatment NPKM, reaching up to 35.9% and 33%, respectively, indicating that this fraction of SOM is probably the major storage pool for SOC and TN, and easily affected by human management practices. Compared with Treatment CK, Treatment NPKM significantly decreased the content of non-hydrolyzable free silt (NH-dSilt) and non-hydrolyzable free NH-dClay by 15% and 9.5%, respectively, in the bio-chemically protected fraction. However, it did not have much effect on the sizes of physico-chemically protected SOM fraction, physico-biochemically protected SOM fraction and chemically protected SOM fraction. All these indicate that these three fractions of SOM are relatively stable, or that they peak or approach to saturation in maintenance capacity. 【Conclusion】 To sum up, this study demonstrates that different functions of SOM respond to long-term fertilization differently. Combined application of organic and inorganic fertilizers is the optimum fertilization measure to enhance the quantity and quality of SOM in the red paddy soil, and the effect is especially obvious on non-protected and physically protected SOM fractions.