Abstract: Jacobi preconditioned conjugate gradient (J-PCG) method based on element-by-element is derived and the calculation process of finite element method (FEM) is presented. The parallelization of the whole calculation process is implemented. A PFEM (Parallel Finite Element Method) program is developed and implemented on a cluster of workstation (COW) with this algorithm. The efficiency on both serial and parallel computer is tested with the case study of a cantilever beam, and it is also applied to FEM analysis of the Ertan arch-dam system. Numerical results show that 3-D finite element method based on element-by-element (EBE) policy utilizes element matrices, thereby avoiding the assembly of global stiffness matrix. Because it requires less memeory storage than conventional finite element solvers on a serial computer, it is very suitable for parallelization. For the parallel analysis of 3-D irregular and complicated structures like arch dams, the finite element EBE method is effective and reliable.