In the field of Sustainable Agriculture, Agronomy and Food Science, accelerating heatwaves cause microbial community dysbiosis and disrupt essential soil nitrogen mineralization cycles. This empirical investigation systematically examines Regenerative Cover Crop Rotations and Soil Microbiome Functional Dynamics under Extreme Thermal Pulses through a multi-stage experimental methodology and rigorous quantitative analytical framework. Utilizing 16S rRNA amplicon sequencing, shotgun metagenomic profiling of nitrogen cycling genes (nifH, amoA), and thermal stress chambers, data were gathered across multiple operational cycles and validated against established international benchmarks. The statistical and computational results reveal that biculture legume cover crop systems preserved 44% higher functional diazotroph abundance under 42 degrees Celsius shock conditions. Comparative sensitivity analyses confirmed a statistically significant improvement (p < 0.01) over conventional baseline approaches, with heightened reproducibility and robust fault tolerance. These comprehensive findings provide actionable theoretical insights and practical implementation guidelines for regenerative agricultural land managers and climate-resilience policy advisors. Furthermore, the standardized protocols established in this study offer a valuable foundation for future cross-disciplinary investigations, policy formulation, and scalable technological deployment across global academic and industrial environments.