<p>Throughout the Cenozoic, cetaceans (odontocetes and mysticetes) underwent multiple radiation events associated with biological innovations and environmental changes, but their impact on ecomorphological disparity and niche occupancy remains poorly understood. In this study, we quantitatively analyzed cetacean disparity and ecospace occupancy over time, integrating morphological and ecological traits. Our results show that major radiation events were linked to substantial reorganization of ecospace occupancy, and taxonomic diversity changes are often decoupled from ecological disparity. The loss of specific ecotypes significantly impacted cetacean taxonomic structure but only partially affected their ecological structure. The land-to-sea transition is best explained by biotic factors, whereas later diversification events align with environmental changes. The Oligocene is a period of ecological innovation, where multiple key ecological strategies evolved. The ecospace once occupied by early diverging cetaceans, toothed mysticetes, and early diverging odontocetes is never reoccupied, indicating a permanent shift in cetacean ecotypes. Ecospace and taxonomic diversity peaked in the Miocene, followed by selective lineages’ loss. Notably, some extant odontocete lineages occupy different ecospace regions than their Miocene counterparts, likely reflecting distinct ecological adaptations. After the Plio–Pleistocene, odontocetes reached their highest levels of ecological disparity, whereas mysticetes declined to their lowest values.</p>