By using the STAR MSU/AMSU version 3.0 monthly brightness temperature data developed by National Oceanic and Atmospheric Administration(NOAA) during 1978 to 2013, with the Ensemble Empirical Mode Decomposition(EEMD) method, the nonlinear trend of monthly global mean brightness temperature of the upper air and time evolution characteristics of brightness temperature climatic trend are estimated, moreover, the result is compared with that using the Classical Linear Regression(CLR) method. Results show that under the background of warming troposphere and cooling stratosphere, the nonlinear evolution features of the brightness temperature derived by EEMD reveal that the warming trend of the troposphere at mid-high level slows down and even there exists a reverse trend in recent years. The tropospheric warming first occurs in the Arctic, and then gradually extends to the lower latitudes in the northern hemisphere. The tropospheric warming in the polar region even extends up to the lower stratosphere. In the southern hemisphere, the troposphere warming in the mid-low latitude is mainly affected by the atmospheric circulation. In addition, there has been an independent warming phenomenon in the Antarctic in recent decade. The stratospheric cooling first appeared in the middle latitude and then extended gradually equatorward and poleward. A significant cooling of the stratosphere has been found in the Antarctic, and then extended to the lower atmosphere. However, since 2000, with the appearance of a more extensive warming in the Antarctic, the stratosphere cooling has been gradually moving to the middle and low latitude regions.