Soil aggregate stability is an important aspect of soil function and health. Fertilization could potentially alter soil properties and thereby affect aggregate stability. To determine which fertilizer is useful for improving soil fertility and stabilizing soil aggregates and thereby reducing soil erodibility, we examined three types of fertilizer, and measured how soil organic carbon, carbohydrates, and related soil properties influenced aggregate stability in eroded Ultisols. Treatments included control (CK), mineral fertilizer nitrogen (N), phosphorus (P), potassium (K) (NPK), fertilizer NPK plus straw (NPKS), and farmyard manure (FYM). Aggregate stability was tested according to Le Bissonnais method, involving three disruptive tests: fast wetting (FW), slow wetting (SW), and mechanical breakdown (WS). Total organic carbon, particulate organic carbon, mineral-associated carbon, and cold-water-soluble carbohydrate, hot-water-soluble carbohydrate, and dilute acid hydrolysable carbohydrate were measured, as well as soil intrinsic properties (including pH, bulk density, iron and aluminum oxides). The 12-year fertilization had a larger effect on aggregate stability and related soil properties in a 0–15 cm soil layer, whereas no effect was evident at a soil depth of 15–40 cm. MWD (mean weight diameter) under the three tests decreased with increasing soil depth. Fertilization, especially farmyard manure evidently improved MWDFW and MWDWS at a depth of 0–15 cm. Slaking was the main mechanism of aggregate breakdown in Ultisols studied, followed by mechanical breakdown. Correlation analysis showed that MWDFW and MWDWS at a depth of 0–15 cm increased with the increase of particulate organic carbon, total organic carbon, hot-water-soluble carbohydrate and pH. Furthermore, their interaction with amorphous iron oxides enhanced aggregate stability against slaking or, with amorphous aluminum oxides, modified aggregate stability against mechanical breakdown. Consequently, particulate organic carbon was the dominant cementing agent for aggregation in Ultisols studied, and its combination with pH, amorphous aluminum oxides, amorphous iron oxides, and free aluminum oxides play a synergetic role in stabilizing soil aggregate. Accordingly, farmyard manure or fertilizer NPK plus straw improved soil fertility and the ability to resist slaking.