Agricultural management practices play an important role in soil structure and fertility. However, there is a lack of knowledge on the effects of long-term fertilization on aggregate structure in the Loess Plateau region in China. This study was devoted to examining the responses of soil aggregate stability and associated structure to fertilizers over 19 years under a soybean (Glycine max L.)-corn (Zea Mays) rotation. Treatments included unfertilized control (CK); nitrogen (N), phosphorus (P), and NP chemical fertilizers; and manure (M) and MN, MP and MNP organic/chemical combinations. The results showed that the water-stable aggregates, mean weight diameter, geometric mean diameter, aggregate state, and aggregate degree decreased in chemical fertilizers (N, P, and NP). However, it increased in all treatments containing manure (M, MN, MP, and MNP) compared to the CK. The changes in dispersion rate and fractal dimension were opposite to those indicators in all treatments. The applications of chemical fertilizers do guarantee an increase in crop yield, but only organic fertilizers significantly improved soil structure. These results suggest that manure’s incorporation into loessial soil is a preferred strategy for sustainable soil management.