In this paper, a propagation matrix method for lossy layered medium with conductive interfaces is presented. Firstly, on the basis of phase matching principle, an approach to calculating the real and imaginary part of wave vector in a lossy layered medium is given for the case of oblique incident plane electromagnetic wave. Since the direction of real and imaginary part of wave vector are different, the plane wave propagating in lossy dielectric layers is inhomogeneous, which extends the traditional propagation matrix method and makes it suitable for the complex lossy medium. Then, the propagation matrix across graphene interface is deduced by using the electromagnetic field boundary conditions, and the analytical expression of the reflection and transmission coefficient for “infinite thin” graphene layer are given. Finally, the propagation matrix of lossy layered medium with conductive interface is obtained by embedding graphene interface into the layered medium, which can be used for fast analyzing the reflection, transmission and propagation of plane wave in composite structure of layered medium and conductive interface. The validity of the proposed method is demonstrated by calculating the single-layered shielding effectiveness of grapheme. The effects of graphene coating on the reflection, transmission and absorption of plane wave in half-space medium and one-dimensional photonic crystal are also investigated. The results show that the graphene layer can enhance surface reflection and optical absorption.