Based on a multi-timescale analysis method—Hilbter-Huang Transform (HHT), inter-annual and inter-decadal variability of the SST in Niňo3 region in the last 100 years is analyzed. The results show that the SST variability involves seven quasi-period oscillations and one century′s climate state. The main period of SST has experienced a significant change in different period. The inter-annual modes of 3—4a and 6—8a have a phase-locked to the ENSO cycle, and the rest of inter-annual and inter-decadal modes contribute significantly to the ENSO events both in amplitude and duration. But the effects of the “cool or warm climate regime” on La Niňa and El Niňo events are not prominent. The “warm” regime is in favor of El Niňo events since 1977 is because the inter-decadal oscillations are very strong in warming phase. It is noteworthy that the amplitudes of three inter-decadal oscillations in warming phase have been weakened since the late 1990s, whose influence on ENSO warm events will be reduced.