Abstract The global push to combat climate change by transitioning to clean power generation is accelerating. One promising avenue involves using hydrogen in place of natural gas in gas turbine-based power plants. While the development of new hydrogen combustors shows potential, advancements in operational technologies are needed to ensure higher hydrogen cofiring with existing combustion systems. In our study, we propose a novel approach called heterogeneous natural gas–hydrogen input: varying hydrogen content between different nozzle groups in gas turbine combustors. Using a full-scale combustor of an F-class gas turbine model, we experimentally investigated the impact of heterogeneous hydrogen concentrations at the center and outer nozzles on combustion dynamics and emissions, comparing these with homogeneous fuel supply cases of 100% natural gas and natural gas–hydrogen mixtures. While hydrogen cofiring did not change the maximum amplitude of combustion dynamic pressure across the total frequency range, peak amplitudes in the 125–245 Hz domain were linearly proportional to the hydrogen cofiring ratio, with a 41.2% increase at 30% cofiring identified as a possible limiting factor. Our findings revealed a significant correlation between NOx emissions and combustion stability under varying levels of heterogeneity. Higher heterogeneity with intensive hydrogen input into the center nozzle improved cofiring performance, reducing the peak amplitude in the limiting frequency domain by 22% for a 25% cofiring ratio, potentially extending the critical hydrogen cofiring ratio. Implementing heterogeneous natural gas-hydrogen inputs emerges as a promising method to enhance combustion stability and enable effective hydrogen cofiring.