Fuel cell is one of the promising candidates for mobile power source. In the fuel cell, the design considering micro structure is considered to be indispensable for developing a highperformance cell. In this work, the effect of the anode electrode structural design of the DMFC (direct methanol fuel cell) on the cell performance was investigated by three-dimensional numerical simulation. The influence of diffusion layer thickness in the electrode on the mass fraction of methanol and carbon dioxide in the reaction layer is examined for various operation conditions. As a result, we clarified that the micro structure change in the electrode significantly affected the mass fraction of the species in reaction layer in the fuel cell.