Abstract: Bacterial diversity in the plough layer is widely regarded as the "second life" of agroecosystems, playing a pivotal role in sustaining maize yield formation and preserving long-term soil fertility. In northern China, the widespread adoption of large-scale mechanized flat-planting practices for maize cultivation has inadvertently introduced moderate to severe soil compaction, particularly in tractor chassis coverage zones. This compaction alters the soil’s physical structure and chemical properties, potentially triggering cascading negative effects on microbial communities. Notably, the response mechanisms of plough layer bacterial diversity to mechanical compaction remain poorly understood, limiting the development of sustainable soil management strategies. To address this knowledge gap, a comprehensive two-year field experiment was conducted in designated plot head areas, focusing on tractor-induced compaction gradients (0, 3, and 7 passes) and soil depth variations. Metagenomic sequencing was employed to systematically evaluate bacterial diversity, abundance, and activity under these conditions, aiming to unravel the ecological consequences of compaction and identify critical thresholds for microbial resilience. The experimental design integrated soil sampling across multiple depths within the plough layer (0–10 cm), targeting both compacted zones and adjacent undisturbed controls. Soil physicochemical parameters, including moisture content, bulk density, were measured to quantify compaction-induced changes. Bacterial community profiles were analyzed using 16S rRNA gene sequencing, with a focus on dominant phyla such as Acidobacteria, Proteobacteria, and Actinobacteria, which are known for their functional roles in nutrient cycling and soil health. Magnitude variance analysis and time series modeling were applied to assess fluctuations in bacterial abundance and community dynamics, while stress response indices were calculated to evaluate microbial recovery potential post-compaction. Results demonstrated that mechanical compaction significantly modified soil physicochemical properties. Seven-pass compaction, for instance, increased bulk density by 12–16%. These changes created a less hospitable environment for aerobic bacteria, leading to marked shifts in community composition. Specifically, Acidobacteria—a phylum associated with oligotrophic conditions—exhibited a 7% reduction in relative abundance under high compaction. Actinobacteria, recognized for their resilience in nutrient-poor environments and ability to degrade complex organic compounds, showed moderate sensitivity, reflecting their capacity to adapt to physicochemical stressors.Time series data further highlighted delayed recovery of bacterial diversity in heavily compacted soils. This impaired resilience was linked to persistent alterations in soil structure, such as reduced macropore connectivity and oxygen diffusion, which disrupted microbial habitat heterogeneity. Stress response models indicated that compaction-induced physicochemical changes exerted selective pressures, favoring stress-tolerant taxa while suppressing functionally sensitive groups. The dominance of stress-adapted taxa under compaction may temporarily stabilize ecosystem functions but could compromise long-term soil health by reducing functional redundancy. To mitigate these risks, the study advocates for precision soil management practices, such as intermittent deep tillage or controlled traffic farming, to alleviate compaction while preserving microbial diversity. These findings carry significant implications for sustainable agriculture. In conclusion, this research elucidates the intricate interplay between mechanical compaction, soil microbiology, and agroecosystem resilience. By bridging soil physics and microbial ecology, it offers a framework for optimizing mechanized farming systems to safeguard the "second life" beneath our feet—the indispensable microbial communities that sustain global food security.