The two-dimensional adjusted Iwan beam element (2-D AIBE) has been developed by the authors to simulate the nonlinear dynamic behavior of bolted joints in 2-D jointed beam structures. The 2-D AIBE consists of two adjusted Iwan models that are arranged to represent two-dimensional beam behavior. In this paper, a three-dimensional adjusted Iwan beam element (3-D AIBE) is presented to represent the 3-D nonlinear behavior of bolted joints. In the 3-D AIBE, the bending behavior of the 3-D beam element in two uncoupled bending planes is addressed by two 2-D AIBEs, respectively. Extension is represented by one adjusted Iwan model; and another adjusted Iwan model accounts for torsion. Impulsive loading experiments are applied to a jointed frame structure and a beam structure containing the same joint. The frame is subjected to excitation out of plane so that the joint is under rotation and single axis bending. By assuming that the rotation in the joint is linear elastic, the parameters of the joint associated with bending in the frame are identified from acceleration responses of the jointed beam structure, using a multi-layer feed-forward neural network (MLFF). Numerical simulation is then performed on the frame structure using the identified parameters. The good agreement between the simulated and experimental impulsive acceleration responses of the frame structure validates the efficacy of the presented 3-D AIBE, and, also, indicates that the model can potentially be applied to more complex structural systems with joint parameters identified from a relatively simple structure.