The inevitable oscillations of the payload decrease the positioning accuracy and lessen the safety in dual cranes carrying a large payload. In the presence of the structural flexibility, the dynamics of dual cranes are governed by the payload swing, pitch, and twisting after considering three-dimensional motions. However, little research has been directed at the modeling and control of three-dimensional dual cranes. A dynamic model of three-dimensional dual cranes including the payload swing, pitch and twisting is described. Moreover, a combined modified extra-insensitive input shaper and four-pieces smoother method is proposed to control the swing, pitch, and twisting of the payload. The dynamic behavior of the nonlinear model and the effectiveness of the new control method are verified experimentally on dual cranes carrying a slender beam.