Abstract: Background Infrastructure development, such as power‐transmission substations, is widely recognised as causing severe soil degradation in arid desert regions. However, evaluating the remediation efficacy of soil amendments—namely organic fertilizer and composite microbial inoculants—is crucial for reconstructing impaired soil microbial ecological functions, restoring ecosystem self-maintenance capacity, and safeguarding regional ecological security. Methods In this study, we evaluated the remediation efficacy of organic fertilizer and microbial inoculant on degraded soils under desert power-transmission substation construction in the Gonghe Basin, combining field trials with high-throughput 16S rRNA gene sequencing. Results (1) Both amendments markedly increased microbial biomass carbon and nitrogen, soil organic carbon, total nitrogen, hydrolyzable nitrogen, β-glucosidase, and leucine-aminopeptidase activities while significantly reducing soil pH, available phosphorus, and Ca²⁺/Mg²⁺ concentrations. (2) Organic fertilizer treatments enriched Actinobacteria, Chloroflexi, and Patescibacteria, whereas microbial inoculant favored Gemmatimonadetes, Proteobacteria, and Chloroflexi; both amendments suppressed Acidobacteria and Bacteroidetes. These treatments also significantly elevated bacterial richness and α‐diversity, with PERMANOVA confirming distinct community structures among treatments (R² = 0.332, P < 0.001). (3) Co-occurrence network analysis revealed increased modularity, clustering coefficient, and negative correlation proportion, alongside reduced average path length and closeness centrality, characteristic of a “small-world” topology and enhanced community robustness. (4) Mantel tests demonstrated strong correlations between bacterial community structure and microbial biomass C/N and key enzyme activities (r > 0.7, P < 0.01), with organic fertilizer‐driven communities primarily influenced by organic C and available N, while inoculant-treated soils were shaped by total K, available P, and available K. Conclusions This study reveals, in a desertified engineering disturbance context, that soil amendments synergistically reconstruct bacterial community structure, boost functional activity, and stabilize network architecture via both physicochemical improvement and targeted microbial interventions, thereby providing critical microbial‐based strategies for ecological restoration in arid infrastructure zones.