It is critically important to study the impacts of chemical and organic fertilizers on soil organic carbon (SOC), because regional carbon sequestration is influenced under long-term farming conditions. We chosed four treatments, i.e. no fertilizer (CK), conventional chemical fertilization (CF), low rate EM compost (EML) and high effective microorganisms compost (EMH) from the long-term experiment (19 a) located in Quzhou County, Hebei Province. Soil samples were taken and separated into different fractions using physical, density and particle size methods for the 0—10, 10—20, 20—60 and 60—100 cm soil layers, and the SOC contents of the whole soil and soil fractions were analyzed. The results indicated that in the 0—10 cm layer, compared with the CK, CF, EML, and EMH all significantly increased SOC content of the whole soil and all fractions by 33% to 63%. In the soil layers deeper than 10 cm, only EML and EMH treatments significantly increased SOC content of the whole soil and all fractions (by 20% to 67%). For the 0–100 cm soil layer, compared with the CK, the SOC stock increasing rate in EMH treatment (1.17 t C /(hm2·a)) was 11.7 folds of that in CF treatment. In the 0—10 cm layer, SOC saturation of the ＜20 μm mineral fraction for CF, EML and EMH treatments (65% to 82%) was significantly higher than that of the CK (64%). In the soil layer deeper than 10 cm, there was no significant difference in SOC saturation among the CK, CF and EML treatment, but EMH treatment had a significantly higher SOC saturation than the other three treatments. We concluded that under long-term fertilization conditions, SOC in soil layers depper than 10 cm should be given more consideration than before. For the North China Plain where has a low level of SOC, there is still much space to improve soil carbon level, and organic fertilizer is one of the most effective farming practices.