The combinatorial mutation of polygons, which transforms a given lattice polygon into another one, is an important operation to understand mirror partners for two-dimensional Fano manifolds, and the mutation-equivalent polygons give ${\mathbb Q}$-Gorenstein deformation-equivalent toric varieties. On the other hand, for a dimer model, which is a bipartite graph described on the real two-torus, one can assign a lattice polygon called the perfect matching polygon. It is known that for each lattice polygon $P$ there exists a dimer model having $P$ as the perfect matching polygon and satisfying certain consistency conditions. Moreover, a dimer model has rich information regarding toric geometry associated with the perfect matching polygon. In this paper, we introduce a set of operations which we call deformations of consistent dimer models, and show that the deformations of consistent dimer models realize the combinatorial mutations of the associated perfect matching polygons.