The present 3D Dataset contains the 3D models analyzed in Bianucci et al. 2023, A heavyweight early whale pushes the boundaries of vertebrate morphology, Nature. These include bones of the holotype of new species Perucetus colossus (MUSM 3248), as well as the articulated skeleton of Cynthiacetus peruvianus (holotype, MNHN.F.PRU10). The latter was used to estimate the total skeleton volume of P. colossus.