Marked chain-order polytopes are convex polytopes constructed from a marked poset, which give a discrete family relating a marked order polytope with a marked chain polytope. In this paper, we consider the Gelfand-Tsetlin poset of type A, and realize the associated marked chain-order polytopes as Newton-Okounkov bodies of the flag variety. Our realization connects previous realizations of Gelfand-Tsetlin polytopes and Feigin-Fourier-Littelmann-Vinberg polytopes as Newton-Okounkov bodies in a uniform way. As an application, we prove that the flag variety degenerates into the irreducible normal projective toric variety corresponding to a marked chain-order polytope. We also construct a specific basis of an irreducible highest weight representation which is naturally parametrized by the set of lattice points in a marked chain-order polytope.