This paper discusses the development of an invariant finite difference scheme to simulate the microphase separation of copolymers in one-dimensional thin liquid films. The film phenomena are modelled using two-phase shallow water equations and the Ohta-Kawasaki potential, which governs the phase separation of the copolymer. Non-positive volume fractions and spurious oscillations are eventually eliminated, in simulating the one-dimensional phase separation lamellar pattern.