Let $d\in\mathbb{N}$ and ${\alpha}\in(0,\min\{2,d\})$. For any $a\in[a^\ast,\infty)$, the fractional Schr\"odinger operator $\mathcal{L}_a$ is defined by \begin{equation*} \mathcal{L}_a:=(-\Delta)^{{\alpha}/2}+a{|x|}^{-{\alpha}}, \end{equation*} where $a^*:=-{\frac{2^{\alpha}{\Gamma}((d+{\alpha})/4)^2}{{\Gamma}((d-{\alpha})/4)^2}}$. In this paper, we study two-weight Sobolev inequalities associated with $\mathcal{L}_a$ and two-weight norm estimates for several square functions associated with $\mathcal{L}_a$.