For nonpremixed combustion, the mixture fraction variables are widely used as a conserved scalar to map out the flame structure in a unified manner. For ammonia–hydrogen flames, however, a proper definition of the mixture fraction variable is difficult due to the presence of fuel-bound nitrogen in ammonia. This work proposes a revised mathematical definition of the mixture fraction as a modified form of the Bilger’s formula in order to describe the characteristics of nonpremixed ammonia–hydrogen blend flames at general fuel mixture ratios. The newly defined mixture fraction properly accounts for differential diffusion effects in the presence of hydrogen, and thus serves as a convenient invariant coordinate for the flame manifolds. Counterflow nonpremixed flames with different ammonia–hydrogen ratios were computed and the validity of the new formulation is demonstrated. The analysis of the flame structure revealed the presence of double reaction zones, one dominated by the hydrogen oxidation and the other by ammonia oxidation. The role of differential diffusion is crucial in determining the existence of double reactive layers and its impact is evaluated by varying the strain rate. Detailed reaction analysis revealed that the hydrogen flame is related to HO2 reactions, while the ammonia flame to N, NH2 and NH3 reaction groups. As the strain rate is increased, OH reactions are responsible for shifting dominant heat release rate from the hydrogen flame to the ammonia flames. The scalar dissipation rate profile shows two distinct peaks, suggesting that a different functional description is needed in the flamelet modeling framework.