Research on ocean internal waves by seismic oceanography is a frontier issue concerned by marine geophysicists and physical oceanographers. The paper applied Empirical Mode Decomposition (EMD) method of a new time-frequency analysis tool- Hilbert-Huang transform for studying vertical displacement data of internal waves in the northeastern South China Sea from seismic data and obtained new results. It showed that the internal waves above the central basin of South China Sea consist of components of different wavelength of around 1.2, 2.5, 4, 12.5 km. The internal waves of the wavelength of 1.2 and 2.5 km are coupled between the upper and the lower part within the depth range of 200~1050 m, while the separated interface located at 600~700 m exists for the internal waves of the wavelength of around 4 and 12.5 km and the phase change is about 90° between the upper and the lower part, which infers oblique propagation of low wave-number internal waves energy. It inferred there is nice potential application of EMD method in seismic oceanography research.