Let $G$ be a finite abelian group of order $n$, and let $\mathsf M(G,m)$ denote the set of zero-sum sequences over $G$ of length $m$. We introduce the zero-sum polytope $\mathcal P_G$, a rational polytope of dimension $n-1$, whose lattice points encode zero-sum sequences: \[ |\mathsf M(G,m)|=|m\mathcal P_G\cap \mathbb Z^n|. \] This naturally realizes the enumeration of zero-sum sequences as a problem in rational Ehrhart theory, which leads to a combinatorial reciprocity theorem identifying the negative evaluations of the corresponding counting quasipolynomial with zero-sum sequences of full support. Our main results establish a face-stratified rigidity for zero-sum polytopes: whenever two such polytopes have equal total lattice point counts at specific dilations, the dimension-wise open-face strata are equinumerous. Moreover, we study the natural $\operatorname{Aut}(G)$-action on $\mathcal P_G$, derive equivariant generating functions and reciprocity formulas, and obtain cyclic sieving phenomena for natural cyclic actions.