A long-term field experiment was carried out in Shenyang, Liaoning Province, northeastern China by using the fractionation techniques of aggregate and soil organic matter (SOM) in order to study the effect of long-term application of fertilizers on organic carbon content of soil intra-aggregate particulate (POM C). The results indicated aggregates <53 μm under long-term fertilization treatment transformed to microaggregate and macroaggregate, which was propitious to the enrichment of POM. The mean coarse POM C contents of inter-microaggregate within 250 ~ 2000 μm macroaggregate under long-term organic manure or combined with inorganic fertilizers increased by 6.97 and 4.85 times respectively compared with the non-fertilization treatment. Fine POM C content changed erratically under different fertilization treatments. Fine POM C content was significantly higher than coarse POM C. In addition, application of organic manure or combined with inorganic fertilizers increased significantly POM C contents of intra-microaggregate within 250 ~ 2000 μm macroaggregate and free intra-microaggregate (except AN treatment), while inorganic fertilizers decreased them by 22.5% ~ 21.1% .