The concept of coupling element in whole transfer matrix method is proposed, the transfer matrix of isotropic coupling element and that of anisotropic coupling element are derived and some numerical examples are given in the paper. The whole transfer matrix method takes the set of state vectors of axes as the systematical state vector, and each rotor transfers the systematical state vector simultaneously to obtain the equations for whole transfer matrix method. Substituting the systematical boundary conditions into the equations of whole transfer matrix method and solving it, the critical speeds of multi-rotor system can be obtained. Comparing with sub-structure transfer matrix method, the whole transfer matrix method is more suitable for engineers because of that the multi-rotor system does not be divided at coupling places and it does not need to construct the balance equations or deformation compatibility equations.