Mode coupling between the operation mode and unwanted eigenmodes has a significant influence on the working performance of novel thin-film magnetoelectric (ME) devices operating at high frequencies. In this article, the extended frequency spectrum quantitative prediction (FSQP) method is used to investigate mode-coupling vibrations in high-frequency ME heterostructures. This method has three key procedures. First, wave propagation in ME heterostructures is studied to determine the wavenumber and frequency of the eigenmodes. Second, the variational formulation of a general ME heterostructure is constructed. Finally, frequency spectra for predicting the coupling strength among the eigenmodes are obtained by substituting the solutions consisting of all eigenmodes into the variational formulation. Two numerical examples are presented to validate the extended FSQP method. The mode shapes of the mechanical displacements are used to thoroughly describe the mode-coupling behavior in different vibration modes. The numerical results show that the mode-coupling strength is significantly affected by the structural size and number of layers in an ME heterostructure. Furthermore, structural symmetry along the thickness direction may cause specific mode-decoupling phenomena. Effective strategies for suppressing multimode-coupling vibrations in ME heterostructures by optimizing the lateral aspect ratios based on the frequency spectra are proposed to guide device design.