In this paper, in order to analyze the dynamic response of a floating crane when it lifts a heavy cargo, the boom of the floating crane is considered as an elastic beam. The boom is divided into elements based on finite element formulation and the floating frame of reference formulation and nodal coordinates are employed to model the boom as a flexible body. As an extension of the previous study, in order to consider spatial motion in waves, the coupled equations of motions of the 6 degree of freedom (DOF) floating crane and 6 DOF cargo are developed based on the flexible multibody system dynamics. The 3 dimensional deformation of the elastic boom is considered with 18 DOF. The dynamic simulation of the floating crane and the cargo is performed under regular wave conditions with various cargo weights. Finally, the effects of the elastic boom on lifting cargo are discussed by comparing the simulation results between the elastic boom and a rigid boom.