Abstract: Bacterial diversity in the plough layer, widely regarded as the "second life" of agroecosystems, can sustain the maize yield for long-term soil fertility. Alternatively, the large-scale mechanized flat-planting has been widely adopted for maize cultivation in northern China. Moderate to severe soil compaction has occurred, particularly in the tractor chassis coverage zones. This compaction can alter the soil’s physical structure and chemical properties, potentially triggering cascading negative effects on the microbial communities. Notably, it is still lacking in the response mechanisms of the plough layer bacterial diversity to mechanical compaction. In this study, a two-year field experiment was conducted for sustainable soil management in the plot head areas. An emphasis was also placed on the tractor-induced compaction gradients (0, 3, and 7 passes) and soil depths. Metagenomic sequencing was employed to systematically evaluate the bacterial diversity, abundance, and activity under these conditions. The ecological consequences of the compaction were used to identify the critical thresholds for microbial resilience. The experimental design integrated the soil sampling over multiple depths within the plough layer (0–10 cm), particularly for both compacted zones and adjacent undisturbed controls. Soil physicochemical parameters, including the moisture content, bulk density, were measured to quantify the compaction-induced variations. Bacterial community profiles were analyzed using 16S rRNA gene sequencing. The dominant phyla were selected, such as Acidobacteria, Proteobacteria, and Actinobacteria, which were known for their functional roles in nutrient cycling and soil health. Magnitude variance analysis and time series modeling were applied to assess the fluctuations in the bacterial abundance and community dynamics. While the stress response indices were calculated to evaluate the microbial recovery potential post-compaction. Results demonstrated that the mechanical compaction significantly modified the soil physicochemical properties. For instance, seven-pass compaction increased the bulk density by 12%–16%. There were the outstanding shifts in community composition, due to the less hospitable environment of the aerobic bacteria. Specifically, Acidobacteria—a phylum associated with oligotrophic conditions—exhibited a 7% reduction in the relative abundance under high compaction. Actinobacteria shared the moderate sensitivity suitable for the physicochemical stressors, which was recognized for their resilience in the nutrient-poor environments to degrade complex organic compounds. Time series data further highlighted that there was a delayed recovery of bacterial diversity in heavily compacted soils. The resilience was altered in the soil structure, such as the reduced macropore connectivity and oxygen diffusion, which disrupted microbial habitat heterogeneity. Stress response models indicated that the compaction-induced physicochemical properties were exerted on the selective pressures, thus favoring stress-tolerant taxa while suppressing functionally sensitive groups. The stress-adapted taxa after compaction temporarily stabilized the ecosystem functions, but the long-term soil health was compromised to reduce the functional redundancy. The precision soil practices mitigated these risks, such as the intermittent deep tillage or controlled traffic farming. As such, the compaction was alleviated to preserve the microbial diversity. These findings can provide significant implications for sustainable agriculture. In conclusion, there was a significant interaction among mechanical compaction, soil microbiology, and agroecosystem resilience. Soil physics and microbial ecology can also be bridged to optimize mechanized farming. The indispensable microbial communities can also be sustained for food security.