A brain-computer interface (BCI) is a communication approach that permits cerebral activity to control computers or external devices. Brain electrical activity recorded with electroencephalography (EEG) is most commonly used for BCI. Noise-assisted multivariate empirical mode decomposition (NA-MEMD) is a data-driven time-frequency analysis method that can be applied to nonlinear and nonstationary EEG signals for BCI data processing. However, because white Gaussian noise occupies a broad range of frequencies, some redundant components are introduced. To solve this leakage problem, in this study, we propose using a sinusoidal assisted signal that occupies the same frequency ranges as the original signals to improve MEMD performance. To verify the effectiveness of the proposed sinusoidal signal assisted MEMD (SA-MEMD) method, we compared the decomposition performances of MEMD, NA-MEMD, and the proposed SA-MEMD using synthetic signals and a real-world BCI dataset. The spectral decomposition results indicate that the proposed SA-MEMD can avoid the generation of redundant components and over decomposition, thus, substantially reduce the mode mixing and misalignment that occurs in MEMD and NA-MEMD. Moreover, using SA-MEMD as a signal preprocessing method instead of MEMD or NA-MEMD can significantly improve BCI classification accuracy and reduce calculation time, which indicates that SA-MEMD is a powerful spectral decomposition method for BCI.