The microstructure of wood plastic composite (WPC) with respect to wood particle content and maleic anhydride-grafted polypropylene (MAHPP) compatibilizer is studied by both linear and nonlinear rheological methods in this article. The complete long characteristic relaxation behavior in linear region, which is closely related to the structure of wood particle aggregates and MAHPP compatibilizing effect at the interface, is limited by observing time. Fortunately, the Fourier transform rheology (FTR) by the stress control mode is found to be an effective method for further investigating the structure with long relaxation time in WPC system. The plateau value of I-31 at high stress and the range of phi(31) are proved to be corresponding to the content of wood particle agglomerates in the WPC melts and the type of interfacial hydrodynamic interaction. The interesting outcomes suggest that MAHPP do has the effect on changing the properties of the heterogeneous interface and confirm the difference of the structure with long relaxation time in WPC can be easily captured by the high sensitive FTR indeed.