In Part I of this series of studies, we demonstrated that the intensification rate of a numerically simulated tropical cyclone (TC) during the primary intensification stage is insensitive to the surface drag coefficient. This leads to the question of what is the role of the boundary layer in determining the TC intensification rate given sea surface temperature and favorable environmental conditions. This part attempts to answer this question based on a boundary layer model and a full-physics model as used in Part I. Results from a boundary layer model suggest that TCs with a smaller radius of maximum wind (RMW) or of lower strength (i.e., more rapid radial decay of tangential wind outside the RMW) can induce stronger boundary layer inflow and stronger upward motion at the top of the boundary layer. This leads to stronger condensational heating inside the RMW with higher inertial stability and is thus favorable for a higher intensification rate. Results from full-physics model simulations indicate that the TC vortex initially with a smaller RMW or of lower strength has a shorter initial spinup stage due to faster moistening of the inner core and intensifies more rapidly during the primary intensification stage. This is because the positive indirect effect of boundary layer dynamics depends strongly on vortex structure, but the dissipation effect of surface friction depends little on the vortex structure. As a result, the intensification rate of the simulated TC is very sensitive to the initial TC structure.