In this paper, a numerical procedure for interaction problem of largely deformed membrane and fluid is proposed. Numerical computations of deformable structures in viscous flows often encounter numerical instability, which arises from incompatibility of boundary conditions on a fluid-structure interface. In this work, two aspects of compatibility condition including the balance of energy on the fluid-structure interface and the coupling algorithm are discussed and measures to improve attainment of them in numerical procedures are proposed. In this work, a finite difference method with overlapped meshes is employed to solve a fluid problem accurately. For a membrane, a finite element approximation with the energy-momentum method for the temporal discretization is applied to ensure the conservation of energy and unconditional numerical stability. Numerical solutions of these two subsystems are coupled by the block Gauss-Seidel method. Numerical results are given to show numerical properties including stability of the proposed procedure.