Let $L:=-\Delta+V$ be the Schrödinger operator on $\mathbb{R}^n$ with $n\geq3$, where $V$ is a non-negative potential satisfying $\Delta^{-1}(V)\in L^\infty(\mathbb{R}^n)$. Let $w$ be an $L$-harmonic function, determined by $V$, satisfying that there exists a positive constant $\delta$ such that, for any $x\in\mathbb{R}^n$, $0<\delta\leq w(x)\leq 1$. Assume that $p(\cdot):\ \mathbb{R}^n\to (0,\,1]$ is a variable exponent satisfying the globally $\log$-Hölder continuous condition. In this article, the authors show that the mappings $H_L^{p(\cdot)}(\mathbb{R}^n)\ni f\mapsto wf\in H^{p(\cdot)}(\mathbb{R}^n)$ and $H_L^{p(\cdot)}(\mathbb{R}^n)\ni f\mapsto (-\Delta)^{1/2}L^{-1/2}(f)\in H^{p(\cdot)}(\mathbb{R}^n)$ are isomorphisms between the variable Hardy spaces $H_L^{p(\cdot)}(\mathbb{R}^n)$, associated with $L$, and the variable Hardy spaces $H^{p(\cdot)}(\mathbb{R}^n)$.
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