Objectives This study aimed to analyze the differences in microbial community structure, diversity, and functions under different soil fertilization measures in reclaimed soils, and to identify fertilization strategies that promote the restoration of microbial communities and soil functionality.

Methods A long-term field experiment was conducted on coal mining subsidence-reclaimed land in Shanxi. After 10 years of reclamation, soil samples were collected from 4 treatments: no fertilization (CK), chemical fertilizer (NPK), combined organic and inorganic fertilizer (NPKM), and undisturbed normal farmland (NL). Metagenomic sequencing and molecular ecological network analysis were employed to examine the diversity, composition, ecological networks, and functional profiles of soil bacterial and fungal communities, as well as their correlations with soil nutrients.

Results 1) Soil bacterial richness indices (ACE and Chao1) followed the order NL>NPKM>NPK>CK (P<0.05), whereas fungal richness indices exhibited the opposite trend: NPK>NPKM>NL>CK (P<0.05). Both NPK and NPKM treatments enhanced bacterial and fungal diversity (Shannon index). For fungal diversity, the order was NL>NPKM>NPK>CK (P<0.05), while bacterial diversity showed no significant difference between NPK and NPKM, and NL showed the highest. Bacterial and fungal communities in the NPKM treatment clustered within the same group as NL, whereas NPK clustered with CK, indicating that the microbial community structure (bacteria and fungi) under NPKM treatment did not significantly differ from normal farmland (NL), while NPK remained distinct from normal farmland. 2) Compared with CK, NPKM significantly increased the relative abundance of bacterial phyla Nitrospirae (1002.84%), Gemmatimonadetes (430.38%), Chloroflexi (378.88%), Verrucomicrobia (289.66%), and Actinobacteria (59.49%), while reducing Proteobacteria (−14.58%), Firmicutes (−72.29%), and Bacteroidetes (−26.79%). Both NPKM and NPK treatments increased the abundance of Mortierellomycetes (870.55% and 652.27%) but decreased that of Ascomycota (−40.85% and −30.99%). The β-diversity of soil microbial communities under NPKM was most similar to that of NL. 3) Compared with CK, NPKM reduced microbial network modularity, and decreased the positive/negative link ratio, indicating enhanced interspecies competition and network complexity. 4) Based on KEGG and CAZy database analyses, both NPKM and NPK treatments increased the abundance of functional genes related to amino acid metabolism, carbohydrate metabolism, lipid metabolism, and nucleotide metabolism compared to CK. The NPKM treatment significantly outperformed NPK in enhancing the functional potential of reclaimed soil microbiota, though it still lagged behind the NL treatment in most functional pathways.

Conclusions Ten years after reclamation, the combined application of organic and inorganic fertilizers (NPKM) outperformed chemical fertilizers (NPK) in improving soil microbial diversity, community stability, and metabolic functions. The microbial community structure under NPKM closely resembled that of undisturbed farmland (NL), but its functional capacity remained below NL levels, necessitating sustained organic-inorganic fertilization. NPKM effectively enriched key functional taxa and strengthened core metabolic pathways, representing an efficient strategy to synchronize the restoration of microbial community structure and function in reclaimed soils. This approach is critical for improving soil quality and ecosystem stability in reclaimed areas.