Let E be a flat complex vector bundle over a closed oriented odd dimensional manifold M endowed with a flat connection ∇. The refined analytic torsion for (M,E) was defined and studied by Braverman and Kappeler. Recently, Mathai and Wu defined and studied the analytic torsion for the twisted de Rham complex with an odd-degree closed differential form H, other than one form, as a flux and with coefficients in E. In this paper, we generalize the construction of the refined analytic torsion to the twisted de Rham complex. We show that the refined analytic torsion of the twisted de Rham complex is independent of the choice of the Riemannian metric on M and the Hermitian metric on E. We also show that the twisted refined analytic torsion is invariant (under a natural identification) if H is deformed within its cohomology class. We prove a duality theorem, establishing a relationship between the twisted refined analytic torsion corresponding to a flat connection and its dual. We also define the twisted analogue of the Ray-Singer metric and calculate the twisted Ray.Singer metric of the twisted refined analytic torsion. In particular, we show that in case that the Hermitian connection is flat, the twisted refined analytic torsion is an element with the twisted Ray-Singer norm one.