In an era of global environmental change, understanding how disturbance affects the dynamics of ecological communities is crucial. However, few studies have theoretically explored the potential influence of disturbance including both intensity and frequency on compositional change over time in communities with stage structure. A spatially explicit, individual‐based model was constructed incorporating the various demographic responses to disturbance of plants at two different growth stages: seedlings and adults. In the model, we assumed that individuals within each stage were demographically equivalent (neutral) but differed between stages. We simulated a common phenomenon that seedlings suffered more from disturbance such as grazing and fire than adults. We showed how stage‐structured communities of seedlings and adults responded to disturbance with various levels of disturbance frequency and intensity. In “undisturbed” simulations, the relationship between average species abundance (defined here as the total number of individuals divided by species richness) and community composition turnover (measured by the Bray–Curtis similarity index) was asymptotic. However, in strongly “disturbed” simulations with the between‐disturbance intervals greater than one, this relationship became unimodal. Stage‐dependent response to disturbance underlay the above discrepancy between undisturbed and disturbed communities. Through a spatially explicit, individual‐based model (IBM), we found divergent temporal turnover patterns observed from undisturbed and strongly disturbed communities, which was explained by the stage‐dependent response to disturbance.