This paper is concerned with the comparison of substructure synthesis methods based on global and local coordinates. The substructure synthesis methods based on the global coordinates were first proposed for the dynamic analysis of complex structure and the substructure synthesis method based on the local coordinates was proposed to solve the dynamic problem of tree-like structure. However, the conceptual difference between two methods in solving the dynamic problem has never been explained. In this paper, a structure consisting of two beams is considered to show the conceptual difference of two methods. The dynamic formulation shows the characteristics and differences of two methods explicitly. The procedure for choosing proper substructure modes in each method is also explained in detail. In addition, the advantage of the substructure synthesis method based on the local coordinate system is discussed based on the numerical example. Numerical examples show how two methods are applied to the addressed problem.