Permeability for 14 solutes of four flat membranes of type 1 atelocollagen prepared by different methods using crosslinking with glutaraldehyde are analyzed by the tortuous capillary pore model with their water contents. The results suggest that aggregation of atelocollagen molecule and crosslinking density in the membrane depend on the preparation condition of the membrane. Microstructure of the membranes is discussed with the results obtained from the analysis with the tortuous capillary pore model referring to the dependency of the solute permeabilities on molecular weight of the solutes. In conclusion, we find that various microstructures including heterogeneous ones, are obtainable by controlling the preparation method of collagen membrane, despite the fact that the collagen membrane was a hydrogel. A collagen membrane prepared by the our method is expected to be applied to hybrid artificial organ needed for controlling mass transfer in it because the collagen membrane has a molecular sieve effect at all molecular weights caused by the microstructure.