Almost all organisms on Earth exhibit ontogenetic niche shifts, which causes great phenotypic variation among individuals and is thus considered to critically mediate community structure and dynamics. In contrast, community ecology has traditionally assumed that species are composed of identical individuals with invariant traits and ignored the potentially important ecological roles of ontogenetic niche shifts. To bridge the gap, here I briefly review ecologically relevant examples which show that basic insights of species-based community theories can be revised by including the ontogenetic perspective. Specifically, I focus on the most representative animals in the study of ontogenetic niche shifts, i.e., fish, insects, and amphibians. Notably, their ontogenetic niche shifts create novel views of community structure: (1) ontogenetic diet shifts of predatory fish couple pelagic and benthic food webs in aquatic systems, (2) ontogenetic shifts in interaction types of pollinating insects couple herbivory and pollination networks in terrestrial systems, and (3) ontogenetic habitat shifts of amphibians and aquatic insects couple aquatic and terrestrial metacommunities at interface areas. Dynamic models of such stage-structured communities suggest that their ontogenetic niche shifts may affect the community resilience and disturbance responses. Exploring more complex systems (e.g., where many species undergo ontogenetic niche shifts several times or continuously) is a future direction, for which describing body size relationships between interacting organisms would be a promising approach. I conclude that both theoretical and empirical advances are needed to facilitate the ontogenetic perspective for better understanding mechanisms underlying biodiversity and ecosystem functioning which are increasingly threatened by anthropogenic disturbance.