Reinforced concrete shell structures have been widely used in a variety of modern engineering applications. It is found from earthquake reconnaissance that reinforced concrete (RC) shell structures, such as nuclear containments, cooling towers, roof domes, shear walls, etc., are the key elements in resisting earthquake disturbances. This paper presents the development of a finite element analysis (FEA) program, SCS-3D, to predict the inelastic behavior of RC shell structures. In the program, a Cyclic Softened Membrane Model (CSMM)-based shell element is developed based on the degenerated shell theory with a layered approach and taking into account the CSMM developed at the University of Houston. To form the FEA program, the constitutive relation modules and the analysis procedure were implemented into a finite element program development framework, OpenSees developed at UC Berkeley. Several large-scale structural tests were employed to validate the developed FEA program, including RC panels subjected to a combination of shear and bending, three-dimensional RC shear wall and cylindrical RC tanks subjected to reversed cyclic loading.