Ensemble empirical mode decomposition (EEMD) method was adopted to study the nonstationary interannual variations of the high temperature days in Nanjing summer. Using the EEMD method, the days of the high temperature in Nanjing during 55 years (1946-2000) can be decomposed into a series of modes, including a quasibiennial oscillation (QBO) component and a 6year component. Among those, the QBO with the larger amplitude has the high correlations with original numbers of the high temperature. In brief, the EEMD method other than the traditional and conventional methods can bring us the isolated characteristics of variations of high temperature days at various time scales for the interannual timescale. Moreover, the above two modes correspond to the different wave trains of the global meridional wind at 200 hPa. The former is over South Asia, the South China Sea, the subtropical western Pacific and the Sea of Japan, the middle latitude of North America, and the high and middle latitudes of the southern Indian and southern Atlantic Ocean, while the latter is over the high and middle latitudes of Eurasia. These relationships are of indicative guidance for the climatic prediction of the high temperature days in Nanjing.