Improving soil aggregate stability through proper fertilization management is essential for crop growth. However, how different fertilization regimes affect soil aggregate stability driven by microorganisms and biological binding agents remains largely unexplored. For this purpose, we conducted a 9-year field experiment involving two soil textures (i.e., loam and clay soils) and five fertilization regimes (i.e., no fertilizer or crop straw return (CK), crop straw return (S), chemical fertilization (N), crop straw return with chemical fertilizer (SN), and crop straw return with chemical fertilizer and 20% nitrogen substituted with chicken manure (SNM)). Mean weight diameter (MWD) of soil aggregates, glomalin-related soil protein (GRSP) content, and microbial community composition were investigated. The SN and SNM treatments had similar MWD, which was 70.08–76.45% higher than the CK, and the S and N treatments had similar MWD, which was 20.35–34.76% higher than the CK, indicating better effects of SN and SNM on the improvement of the soil aggregate stability than the S or N treatment. High easily extractable GRSP and total GRSP contents contributed to the improved MWD. Meanwhile, some specific keystone genera identified from the keystone modules (co-occurring groups of soil biota including arbuscular mycorrhizal fungi, bacteria, and nonmycorrhizal fungi) were recognized as the important factors regulating the MWD, though the selected specific genera in the loam soil differed from the clay soil. Altogether, our results highlighted the fundamental role of the GRSP and selected specific keystone microbial taxa in improving the soil aggregate stability and provided a list of microbial taxa linking to MWD in different soils, which could be specifically targeted in specific soil.