In this paper, the characteristic of intrinsic mode function(IMF) and its orthogonalization of ensemble empirical mode decomposition(EEMD), which is often used in the analysis of the non-linear or non-stationary signal, has been studied. In the decomposition process, the orthogonal IMF of EEMD was obtained by applying the Gram-Schmidt(G-S) orthogonalization method, and was compared with the IMF of orthogonal EMD(OEMD). Two signals for comparison analysis are adopted as the analytical test function and El Centro seismic wave. These target signals were compared by calculating the index of orthogonality(IO) and the spectral energy of the IMF. As a result of the analysis, an IMF with a high IO was obtained by GSO method, and the orthogonal EEMD using white noise was decomposed into orthogonal IMF with energy closer to the original signal than conventional OEMD.