The most intense El Niño episodes in more than a century occurred after the 1970s climate shift. Previous studies show that the characteristics of the El Niño-Southern Oscillation (ENSO) phenomenon changed synchronously with the shift, but the associated causes are not fully understood. An analysis of the observed tropical Pacific sea surface temperature (SST) anomalies shows that their increase in the eastern part of the basin after the 1970s is not related to the canonical ENSO pattern, but to the tropical Pacific meridional mode (TPMM). We present observational evidence which supports the hypothesis that the change in the TPMM was triggered by the great salinity anomaly (GSA), which manifested in the North Atlantic during the late 1960s. The GSA induced a weak Labrador convection and a SST dipole south of Greenland. The associated atmospheric structure includes a North Pacific Oscillation sea level pressure dipole in the Pacific sector. This excites the TPMM which contributes to the intense El Niño events and to the enhanced ENSO’s asymmetry, observed after the shift. Our results imply that, if the GSA has not an anthropic origin, as was suggested, then the tropical Pacific climate shift has a natural origin. This is supported by the end of the North Atlantic regime in the 1990s and by the rebound of the tropical Pacific after 1998.