An assembly simulation apparatus and method for a wooden structure are provided. The assembly simulation apparatus for a wooden structure includes an element analysis unit for analyzing shapes of a plurality of elements constituting a three-dimensional (3D) wooden structure model and a coupling relation between the elements. A relation graph generation unit generates a relation graph based on the analyzed shapes of the plurality of elements and the analyzed coupling relation between the elements. An animation creation unit creates an animation of a movement path depending on a task for coupling or separating the plurality of elements, based on the generated relation graph. An animation play unit simulates an assembly method for the wooden structure by playing the created animation depending on the assembly method for the wooden structure.