A comparative study of the structure and transport properties of porous aluminum oxide films obtained by single- and two-step anodization was carried out. It is shown that the oxidation regime significantly affect the number of dead-ended channels, which results in more than twice the variation in membrane permeability. The effect is explained by multiple branching of channels on the initial stages of organization of the porous structure. Branching also occurs on later stages governing mass transport properties of porous anodic alumina films. A model describing transport properties of anodic aluminum oxide membranes based on pore branching on domain boundaries was suggested to fit experimental results of permeance of membranes obtained by both single- and two-step anodization.