Ammonia as a chemical storage carrier for hydrogen has the advantages of high hydrogen storage density and easy storage. However, reconversion of ammonia to pure hydrogen requires additional energy consumption and complex equipment, thus greatly reducing its advantages as a hydrogen storage carrier. The development of PEMFC that use ammonia decomposition gas directly as fuel can avoid the purification of hydrogen and simplify on-site hydrogen production systems. Thus, the application of fuel cells can be greatly expanded. In this paper, a three-dimensional simulation model of PEMFC using ammonia reforming gas as fuel is established based on experimental data. The distribution of local current density and local hydrogen concentration inside the fuel cell and the relationship between them are studied and analyzed. The optimal efficiency and fuel utilization of the fuel cell under different flow rates are investigated. Finally, a preliminary simulation analysis of the effect of anode runner length on the maximum output power of the fuel cell is conducted. The results of the study can provide a reference for the fuel control strategy of ammonia reforming gas-fueled PEMFC and the optimization of the fuel cell.