The key physical processes responsible for inner-core structural changes and associated fluctuations in the intensification rate for a recent, high-impact western North Pacific tropical cyclone that underwent rapid intensification (Nepartak, 2016) are investigated using a set of convection-permitting ensemble simulations. Fluctuations in the inner-core structure between ring-like and monopole states develop in 60% of simulations. A tangential momentum budget analysis of a single fluctuation reveals that during the ring-like phase, the tangential wind generally intensifies, whereas during the monopole phase, the tangential wind remains mostly constant. In both phases, the mean advection terms spin up the tangential wind in the boundary layer, whereas the eddy advection terms deepen the storm’s cyclonic circulation by spinning up the tangential wind between 1.5 and 4 km. Further calculations of the azimuthally-averaged, radially-integrated vertical mass flux suggest that periods of near-constant tangential wind tendency are accompanied by a weaker eyewall updraft, which is unable to evacuate all the mass converging in the boundary layer. Composite analyses calculated from 18 simulations produce qualitatively similar results to those from the single case, a finding that is also in agreement with some previous observational and modelling studies. Above the boundary layer, the integrated contribution of the eddy term to the tangential wind tendency is over 80% of the contribution from the mean term, irrespective of inner-core structure. Our results strongly indicate that to fully understand the storm’s three-dimensional evolution, the contribution of the eddies must be quantified.