The composition and fractal dimension (D) of micro-aggregates in 0~20 cm soil layer were studied on a long-term fertilized field under wheat-maize cropping rotation in North China Plain, and relationships of soil fertility with compositional proportion of characteristic soil micro-aggregates (PCM, ＜20 μm/(250~20) μm), ratio of the content of ＜20 μm particle-size to the content of 2 000~20 μm particle-size content in soil micro-aggregates determination (RMD, ＜20 μm/(2 000~20) μm) and D were evaluated. The long-term fertilization experiment was designed to include 7 treatments: fertilizer NPK (NPK), organic manure (OM), half organic manure with chemical fertilizer NPK (1/2OMN), chemical fertilizer NP (NP), chemical fertilizer PK (PK), chemical fertilizer NK (NK) and control (CK). After 18 years of fertilization, all the treatments, except CK showed lower values of PCM, RMD and D, and higher nutrients content and enzyme activity. Among the fertilization treatments, Treatment OM was the lowest in PCM、RMD and D, followed by Treatment 1/2OMN, and the treatments with chemical fertilizers. Balanced application of fertilizers (Treatment NPK) was lower in PCM、RMD and D than imbalanced use of fertilizers (Treatments NP, PK, and NK). PCM, RMD and D were closely related to crop yield, soil organic matter, hydrolysis N, and enzyme activity. The findings indicate that the use of organic manure alone or in combination with fertilizer NPK and balanced application of fertilizer NPK are key to improving soil micro-aggregate composition, decreasing PCM, RMD and D, and increasing soil nutrient preserving and supplying capacity; and that PCM, RMD and D can be used as integrated quantitative indexes to evaluate the soil fertility under a long-term fertilization cropping system.