The Levins model is a classical but still widely used metapopulation model that describes temporal changes in the regional abundance of a species by extinction and colonization of subpopulations. A fundamental assumption of the model is that the landscape is homogeneous and the species moves between identical patches at random. However, this assumption clearly contrasts with the common observation that different stages prefer or require different habitat types. Here I studied a minimum extension of the Levins model in which the species has stage-specific (juvenile and adult) spatial distributions and dispersal occurs at the timing of reproduction and maturation (i.e., ontogenetic habitat shifts). I examined how the persistence of the stage-structured metapopulations would be affected by rescue effect and interspecific competition. The models predict that rates of ontogenetic habitat shifts are particularly crucial for the persistence or coexistence of stage-structured metapopulations because the species need to complete biphasic life cycles. The present study opens a new avenue for exploring stage- and space-structured population dynamics and will contribute to better landscape management for the conservation of stage-structured animals.