Abstract: Empirical mode decomposition (EMD) method is applied to the atmospheric dynamical system that interacts between the basic flow and the waves, the intrinsic mode functions (IMF) are separated to the solution series of the stream function to the different system states, and the relation between the system state and the IMF is analyzed, and realized streamfunction vacillation structure. The results show that along with the more complicated system, the IMF's numbers which are formed of the solution series correspondingly increases. As for the Hadley flow, each IMF of all components of the stream function Ψ is all going to zero equal line; as for the Rossby flow, Ψ components are mainly formed by a high frequency IMF with periodicity; as for the vacillate state, Ψ components are mainly formed by two or three high frequency IMFs with periodicity; as for the non-period stream, Ψcomponents areformed by many IMF's with no period; as for the multi period and non period states, the same compnent can be formed by period and nonperiod vacillation waves. Low frequency IMF components show the long time change of Ψ series.