Based on continuum mechanics and the principle of virtual displacements, incremental total Lagrangian formulation (T.L.) and incremental updated Lagrangian formulation (U.L.) were presented. Both T.L. and U.L. considered the large displacement stiffness matrix, which was modified to be symmetrical matrix. According to the incremental updated Lagrangian formulation, small strain, large displacement, finite rotation of three dimensional Timoshenko fiber beam element tangent stiffness matrix was developed. Considering large displacement and finite rotation, a new type of tangent stiffness matrix of the beam element was developed. According to the basic assumption of plane section, the displacement field of an arbitrary fiber was presented in terms of nodal displacement of centroid of cross-area. In addition, shear deformation effect was taken account. Furthermore, a nonlinear finite element method program has been developed and several examples were tested to demonstrate the accuracy and generality of the three dimensional beam element.