Abstract: The multi-layer shell element is widely used for the numerical simulation of engineering structures because of its simple model and clear physical property. An efficient nonlinear analysis model for the multi-layer shell element is proposed based on the theory of the inelasticity-separated finite element method (IS FEM), in which the section deformation of the element is decomposed into linear elastic and nonlinear components, and the nonlinear deformation field is established by using Gaussian integration in the middle of the element as the interpolation point. Based on the principle of virtual work, a governing equation for the multi-layer shell element with the IS FEM form is derived by treating the decomposed nonlinear deformation as additional degrees of freedom. Moreover, the governing equation can be solved efficiently by incorporating the combined approximations method into Woodbury formula. The time complexity theory is used to evaluate the computational efficiency of both the proposed method and the conventional finite element method, and the results show that the present method has significant advantages in structural nonlinear analysis. Finally, two numerical examples are used to verify the accuracy and efficiency of the proposed algorithm by comparing the results with ANSYS results.