We present in this paper a finite element formulation for nonlinear torsional analysis of 3D beams with arbitrary composite cross-sections. Since the proposed formulation employs a continuum mechanics based beam element with kinematics enriched by the extended St. Venant solutions, it can precisely account higher order warping effect and its 3D couplings. We propose a numerical procedure to calculate the extended St. Venant equation and the twisting center of an arbitrary composite cross-section simultaneously. The accuracy and efficiency of the proposed formulation are thoroughly investigated through representative numerical examples.