The effect of anode gas channel height on gas diffusion and cell performance in a 100 $cm^2$ class molten carbonate single cell is investigated. Single cell separators with three different channel height are used. The effect of the gas channel height on the distribution of the reactive gas concentration is evaluated by the two-dimensional concentration diffusion equation. The overpotential caused by concentration drop with different channel height is estimated by the voltage decay related to diffusion of reactants, well known as concentration polarization, using limiting current density. The estimation could have the possibility to identify the reactant mass transfer polarization in the complicate factors of the overall electrodes.