This study focuses on improving the heat transfer and emission characteristics in a methanol-ammonia combustion system for a hydrogen production reactor. By mixing methanol with ammonia, flame stability is ensured, and convective heat transfer is enhanced, improving the thermal transfer efficiency of the combustion system. Optimizing the ammonia mixing ratio and equivalence ratio is crucial for enhancing combustion efficiency and controlling emissions. The research findings highlight the impact of oxy-fuel and fuel-rich combustion on combustion efficiency, heat output, and emission levels. When using a 90% ammonia mixing ratio and an equivalence ratio of 0.8, the fuel input energy decreases significantly compared to pure methanol combustion. Although CO2 and NO emissions increase slightly in this scenario, CO emissions decrease substantially, indicating a shift towards low-carbon and efficient combustion. The study underlines the potential of methanol-ammonia mixtures as carbon-neutral energy solutions, offering insights into the importance of proper adjustments for optimal performance in hydrogen production reactors.