We study certain orientation-preserving involutions on three-dimensional small covers. We prove that the quotient space of an orientable three-dimensional small cover by such an involution in $\mathbb{Z}_2^3$ is homeomorphic to a connected sum of copies of $S^2 \times S^1$. If this quotient space is a 3-sphere, then the corresponding small cover is a two-fold branched covering of the 3-sphere along a link. We provide a description of this link in terms of the polytope and the characteristic function.