In the present paper, we prove that the $C_{0}$-semigroup generated by a Schrödinger operator with drift on a complete Riemannian manifold is approximated by the discrete semigroups associated with a family of discrete time random walks with killing in a flow on a sequence of proximity graphs, which are constructed by partitions of the manifold. Furthermore, when the manifold is compact, we also obtain a quantitative error estimate of the convergence. Finally, we give examples of the partition of the manifold and the drift term on two typical manifolds: Euclidean spaces and model manifolds.