Hydrogen is crucial for achieving SDGs by driving energy transition and combating climate change. Proton exchange membrane fuel cell technology, leveraging hydrogen, faces challenges in meeting high‐power demands. The multistack fuel cell system (MFCS) tackles this by integrating multiple substacks, yet its air supply needs meticulous control. Proportional integral derivative (PID) decoupling from single‐stack falls short of MFCS. This article proposes nonlinear model predictive control (NMPC) for optimized air flow and pressure decoupling. Modeling MFCS's air system and designing a predictive model, it is aimed to ensuring precise control of air flow and pressure in each substack. The decoupling experiments show that NMPC outperforms PID, accurately managing air flow and pressure and reducing load fluctuations. For air mass flow, NMPC cuts mean‐absolute error (MAE) by 64.56% and root‐mean‐square error (RMSE) by 81.36%. For pressure, MAE drops 81.23% and RMSE 83.59%. Comprehensive step load tests confirm NMPC's precise, dynamic regulation too, compared to PID, NMPC lowers average MAE for air mass by 20.67%, pressure by 32.22%. RMSE improvements of 31.08% and 33.23% highlight NMPC's strength. NMPC's quick response mitigates coupling issues, enhancing vehicle load adaptability.