A field experiment was conducted to examine the influence of various organic materials on soil aggregate stability and soil microbiological properties on the Loess Plateau of China. The study involved seven treatments: no fertilizer (CK); inorganic N, P, K fertilizer (NPK); low amount of maize stalks plus NPK (LSNPK); medium amount of maize stalks plus NPK (MSNPK); high amount of maize stalks plus NPK (HSNPK); maize stalk compost plus NPK (CNPK); cattle manure plus NPK (MNPK). The organic fertilizer treatments improved soil aggregate stability and soil microbiological properties compared with CK and NPK treatments. Compared with the NPK treatment, soil treated with LSNPK had a significant increase of 27.1% in 5–3 mm dry aggregates. The > 5 mm water stable aggregates treated with CNPK increased by 6.5% compared to the NPK. Soil microbial biomass C and N and urease activity were significantly increased in CNPK by 42.0, 54.6 and 19.8%, respectively. The study indicated that the variation trend in the amount of soil aggregate (0.5–5 mm) for organic fertilizer treatments was similar to the content of soil microbial carbon and nitrogen and soil enzyme activity. Considering the great availability of organic material, especially stalk compost in this region, application of organic materials is recommended to improve soil structure and fertility.