We prove a robust contraction decomposition theorem for $H$-minor-free graphs, which states that given an $H$-minor-free graph $G$ and an integer $p$, one can partition in polynomial time the vertices of $G$ into $p$ sets $Z_1,\dots,Z_p$ such that $\operatorname{tw}(G/(Z_i \setminus Z')) = O(p + |Z'|)$ for all $i \in [p]$ and $Z' \subseteq Z_i$. Here, $\operatorname{tw}(\cdot)$ denotes the treewidth of a graph and $G/(Z_i \setminus Z')$ denotes the graph obtained from $G$ by contracting all edges with both endpoints in $Z_i \setminus Z'$. Our result generalizes earlier results by Klein [SICOMP 2008] and Demaine et al. [STOC 2011] based on partitioning $E(G)$, and some recent theorems for planar graphs by Marx et al. [SODA 2022], for bounded-genus graphs (more generally, almost-embeddable graphs) by Bandyapadhyay et al. [SODA 2022], and for unit-disk graphs by Bandyapadhyay et al. [SoCG 2022]. The robust contraction decomposition theorem directly results in parameterized algorithms with running time $2^{\widetilde{O}(\sqrt{k})} \cdot n^{O(1)}$ or $n^{O(\sqrt{k})}$ for every vertex/edge deletion problems on $H$-minor-free graphs that can be formulated as Permutation CSP Deletion or 2-Conn Permutation CSP Deletion. Consequently, we obtain the first subexponential-time parameterized algorithms for Subset Feedback Vertex Set, Subset Odd Cycle Transversal, Subset Group Feedback Vertex Set, 2-Conn Component Order Connectivity on $H$-minor-free graphs. For other problems which already have subexponential-time parameterized algorithms on $H$-minor-free graphs (e.g., Odd Cycle Transversal, Vertex Multiway Cut, Vertex Multicut, etc.), our theorem gives much simpler algorithms of the same running time.