Aims <p>This study aimed to explore changes in soil microbial co-occurrence networks and functional potential, and reveal the mechanisms driving maize yield improvement under 14-year fertilization.</p> Methods <p>Treatments included no nitrogen (CK), urea (U1/U2, 200/100&#xa0;kg N ha⁻¹), manure (M1/M2, 200/100&#xa0;kg N ha⁻¹), and manure plus urea (U2M2). We determined soil nutrients, enzyme activities, bacterial and fungal community compositions, network properties, functional potentials, and maize grain yield.</p> Results <p>The 14-year fertilizer treatments significantly increased soil nutrients and led to a yield increase of 12%–127%. Manure application exhibited higher edge counts, average degree, and network density, indicative of enhanced microbial network complexity; whereas urea treatment increased modularity and the proportion of negative correlations, suggesting greater microbial network stability. The U2M2 integrated the topological characteristics of both, exhibiting high levels of these complexity- and stability-related indices in microbial co-occurrence networks. Long-term fertilization reduced the functional potential of nitrogen cycling while promoting carbon cycling, with manure substitution showing superior performance. Manure substantially raised the abundance of ectomycorrhizal fungi, while urea markedly boosted arbuscular mycorrhizal fungi. Nitrospirota, which were highly abundant in U2M2, were closely associated with high maize yields. Furthermore, bacterial biomarkers (<i>Nitrospira</i>, <i>MND1</i>, <i>TRA3-20</i>) and fungal biomarkers (<i>Mortierella</i>, <i>Chaetomium</i>, and <i>Podospora</i>) identified in U2M2 showed positive correlations with soil nutrients level, enzyme activity, and yield.</p> Conclusions <p>The manure substitution of 50% urea (U2M2) enhances soil nutrient availability and achieves high crop productivity by increasing microbial diversity and altering the composition and network properties of microbial communities.</p>