The soil-water retention curve (WRC), applied in hydrology, agronomy, and ecology, is an important soil parameter for assessing soil quality and soil functions. Agricultural practices influence WRC by modifying other soil properties, such as soil organic matter content and aggregation. In this study, we investigated the changes in WRC among aggregate fractions as related to fertilizer management in the 0- to 10-cm layer of a paddy soil. The long-term experiment was established in 1986 with five fertilizer treatments: no fertilizer, chemical fertilizer alone, rice residues plus chemical fertilizer, low manure rate plus chemical fertilizer, and high manure rate plus chemical fertilizer. The results demonstrated that at larger water suctions (pF >1.6), the shapes of WRC for different aggregate fractions were similar, but larger aggregates (>2 mm) retained more water than smaller ones (<2 mm). Intra-aggregate water retention capacity was closely related to the interaction of aggregate mineralogy and organic carbon content, as the larger aggregates had lower sand content and higher silt and organic carbon contents than the smaller ones. Under the intensive rice-rice-barley cropping system, joint application of organic materials and chemical fertilizer improved aggregate water retention capacity, but the change of aggregate water retention from chemical fertilizer alone was not significant.