In Part II of this study, the influence of oceanic cold core eddy on the atmospheric boundary layer structures of Typhoon Francisco (2013) is investigated, as well as a comparison with the cold wake effect. Results show that the eddy induces shallower mixed-layer depth and forms stable boundary layer above and near it. The changes of these features shift from northwest to southeast across the storm eye, following the translation of Francisco over the eddy. Nonetheless, the decrease in mixed-layer depth and formation of stable boundary layer caused by the cold wake are located at right rear of the storm. The sensible heat fluxes at the lowest atmospheric model level are mostly downward over the sea surface cooling region. Due to their different relative locations with Francisco, the diabatic heating in the northwest quadrant of the storm can be more effectively inhibited by the cold core eddy than by the cold wake. The asymmetric characteristics of surface tangential wind are less sensitive to sea surface cooling than those of surface radial wind, implying a change in surface inflow angle. Different from previous studies, the surface inflow angle is found to be reduced especially above the cold core eddy and cold wake region. An analysis of radial wind tendency budget indicates that the decrease in radial pressure gradient is dominant in changing the acceleration rate of surface radial wind, rather than the decrease in the Coriolis and centrifugal forces, and therefore more outward surface flow is induced by both the cold core eddy and cold wake.