The present study aims to provide an in-depth analysis of combustion–reaction interactions in an industrial-scale autothermal reformer (ATR) used for hydrogen production. A three-dimensional computational fluid dynamics (CFD) framework was created that includes a non-premixed combustion model and a catalytic reforming bed, effectively simulating heat and mass transfer between the two zones. Detailed methane oxidation kinetics and methane steam reforming kinetics were implemented using user-defined functions (UDFs). Validation against industrial measurement data from Kimia Petrochemical Company showed deviations of less than 8% in both temperature and composition, confirming the model’s reliability. The results indicated that an optimal steam-to-carbon ratio of 1.9 increased hydrogen yield by 33%, while an oxygen-to-methane ratio of 0.66 provided the best synthesis gas composition for methanol production. Design optimization suggested extending the combustion zone by 50 cm and modifying the burner geometry to mitigate hot spots and catalyst damage. These findings provide practical benchmarks for improving ATR performance, thermal management, and catalyst durability in industrial hydrogen and methanol plants. This study integrates a detailed nonpremixed combustion model with a catalytic reforming section within a single CFD platform, offering new insights into industrial-scale ATR design optimization and a detailed elementary combustion mechanism.