Increasing temperatures are a concern for global agriculture because they inhibit the activity of the Nitrogenase enzyme, which is crucial for N2 fixation. The study reveals how the nitrogenase Mo-Fe α subunit adapts to high temperatures by comparing thermophilic and mesophilic bacteria. The Molecular Dynamics simulations study of Acetivibrio thermocellus and Endomicrobium povitum explores how specific amino acids, a higher aliphatic index, and increased RMSD, RMSF, hydrogen bonds, and secondary structure content boost thermostability. A. thermocellus preserves a more compact, stable structure under heat stress. These structural features enable the engineering of heat-tolerant nitrogenase, boosting sustainable agriculture in warm-climate regions.