Formation, distribution and contributing rates of aggregates to organic carbon in black soil in a 28-year long-term fertilization experiment were explored with the physical fractionation method. Results show application of organic fertilizer promoted formation of large-sized aggregates (>0.25 mm), especially 2～1 mm fraction, while combined application of chemical and organic fertilizer did the formation of <1 mm fraction, particularly 0.5～0.25 mm fraction. Fertilization, no matter chemical or organic, increased organic carbon content in the soil, however, the effect of combined application of organic and chemical fertilizers was better than that of the application of either organic or chemical fertilizer. Distribution of organic carbon in aggregates formed two peaks, one in 2～1 mm fraction and the other in 0.25～0.053 mm fraction. In fertilization treatments, no matter organic, chemical and combined, the contribution of 0.5～0.25 mm fraction to organic carbon in the soil was greater than in CK, while application of organic fertilizer alone did more than CK the contribution of 1～0.5 mm fraction. However, in the case of the typical black soil in Northeast China, 2～1 mm and 0.25～0.053 mm fractions contributed the greatest to the protection of organic carbon in the soil, suggesting that the effect of aggregates protecting organic carbon in the soil is the result of the integration of distribution and mineralization of organic carbon. It is, therefore, feasible to effectively preserve soil qualify and fertility by choosing types of fertilizers.