This study focuses on the evaluation of the influence of membrane structure on protein mass transfer through membranes with micro-pore. Transient diffusion fields of protein through three types of micro porous membranes of which have different pore size and same pore cross-sectional area ratio were quantitatively visualized by phase shifting interferometer, and penetrated mass and mass flux were evaluated. Numerical simulations were also performed for varying the pore size. Even under the condition that the channel area for protein transfer was the same, penetrated mass and mass flux were affected by the pore size.