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Finite element analysis for large-scale complicated structure such as aluminum reduction cell makes higher demand on memory capacity and calculation speed, which often results in failure or inefficiency of traditional serial computation for such large-scale problems. Finite element EBE-PCG algorithm is proposed on the basis of EBE(Element-By-Element) idea and Jacobi preconditioned conjugate gradient(PCG) method. The main difficulties in parallel implementation of this algorithm are discussed and solved, such as data organization of grid model, mixed elements processing and data communication. Subsequently, parallel program of finite element analysis based on EBE-PCG is developed using C language and MPI standard library, and then applied to numeric simulation of electric field distribution in aluminum reduction cell. The computational accuracy of parallel program developed is verified through comparison with commercial finite element software ANSYS. Experiment results show that the method is of very high parallel efficiency and can greatly shorten the calculation time, which indicates the effectiveness of EBE's use in parallel computation of large-scale complicated structures.