Soil aggregates and soil nutrients are two important indicators in soil fertility evaluation. Different sizes of aggregates play various roles in the maintenance, availability and transformation of nutrients. This paper compared the effects of long-term fertilization on the distribution of soil aggregates and soil nutrients in aggregates in order to evaluate the role of long-term fertilization on improving soil fertility. The results showed that long-term fertilization decreased the amount of ＞5 mm aggregates but increased the percentage of 0.25 - 5 mm aggregates, thus improved soil structure. Macroaggregate could maintain soil nutrients because it held large amount of soil total C, total N and total P. The effect of fertilization on soil available nutrient was remarkable, soil available N increased with the decrease of aggregate size, which was in favor of plant absorption. In addition, the contribution rate of microaggregates to soil nutrients was intensified with fertilizer application, which was also beneficial for nutrients’ uptake. However, microaggregates were unfavorable to preserve total N and total P with the combination of inorganic fertilizer and organic fertilizer.