The 1997-98 and 2015-16 El Niños were strongest over the past several decades, but had significantly different impacts on biogeochemical fields in the equatorial Pacific. We used a validated physical-biogeochemical model to investigate the differences in biogeochemical responses during the two El Niños. Nutricline was titled along the equator during the 2015-16 El Niño but flat during the 1997-98 El Niño, leading to a significant reduction of nutrient supply (by >80%) in the central equatorial Pacific during the 2015-16 El Niño but in the whole basin during the 1997-98 El Niño. As a result, phytoplankton biomass, especially large-size phytoplankton, primary production and export production showed a basin-scale decrease during the 1997-98 El Niño but a reduction mainly confining to the central equatorial Pacific during the 2015-16 El Niño. There was also a large difference in responses of ecosystem structure to the two El Niños, e.g., decrease in large-size phytoplankton proportion of total phytoplankton biomass occupying the whole basin during the former (with a larger magnitude) but only reaching the central basin during the latter (with a smaller magnitude), which was largely attributed to the more seriously oligotrophic condition during the 1997-98 El Niño. The reduction of nutrient supply and most related biological responses started appearing in the central basin in the development phase of the two El Niños, with a slightly larger magnitude during the 2015-16 El Niño, which was partly attributed to the residual effects of 2014-15 El Niño. The less extent (basin-wide expansion) of oligotrophic waters during 2015-16 El Niño (1997-98 El Niño) might be partly attributed to the cold (warm) phase of Pacific Decadal Oscillation that caused a tilted (flat) thermocline and nutricline in the equatorial Pacific.