Soil degradation in intensive greenhouse vegetable fields is a major agricultural concern since these soils are widely used for food production. Organic materials play essential roles in soil aggregate stability and carbon sequestration. We conducted a 5-year fertilization study in intensively farmed greenhouse vegetable fields to examine the effects of added organic matter on soil aggregate stability, organic carbon fractions and their interrelationships. Four experimental treatments were included: 1) mineral fertilizer only (CK); 2) mineral fertilizer combined with chicken manure (CM); 3) rice husks (RH); and 4) chicken manure plus rice husks (MH). These organic materials applications significantly improved the proportion of > 0.25 mm aggregates while decreasing the ratio of soil < 0.25 mm aggregates. The mean weight diameters of water-stable soil aggregates was increased with organic fertilizer addition and were ranked RH ≈ MH > CM > CK. The organic materials applications treatments had a greater soil organic matter, humic acid and humus than the CK. RH addition significantly increased the proportion of >2 mm aggregates, possibly due to higher humus and polysaccharide carbon content. CM application increased soil Fe-ox content due to soil acidification and increased aliphatic carbon content that in turn increased the proportion of 1-2 mm aggregates. The study indicated a possible advantage for chicken manure and rice husk incorporation for the generation and persistence of stable soil aggregates.