In this paper, extending our previous joint work (Hu et al., Math Nachr 291:343--373, 2018), we initiate the study of Hopf hypersurfaces in the homogeneous NK (nearly K\"ahler) manifold $\mathbf{S}^3\times\mathbf{S}^3$. First, we show that any Hopf hypersurface of the homogeneous NK $\mathbf{S}^3\times\mathbf{S}^3$ does not admit two distinct principal curvatures. Then, for the important class of Hopf hypersurfaces with three distinct principal curvatures, we establish a complete classification under the additional condition that their holomorphic distributions $\{U\}^\perp$ are preserved by the almost product structure $P$ of the homogeneous NK $\mathbf{S}^3\times\mathbf{S}^3$.