Based on a long-term simulation of an ocean-biogeochemical coupled model, we investigate the biogeochemical response to the two types of El Niño events, a Cold Tongue (CT)-El Niño and a Warm Pool (WP)-El Niño, in which a local maximum of anomalous sea surface temperature (SST) is located in the eastern and central tropical Pacific. Our model is able to reasonably simulate the characteristics of the biological variables in a way comparable to the observations. During the developing period, anomalous low chlorophyll appears in the eastern Pacific, while it appears in the central Pacific in the WP-El Niño. The difference in the spatial-temporal response of chlorophyll for the two types of El Niño events is mainly due to the eastward zonal advection of upper ocean currents, which plays a role in bringing nutrient-poor water from the western Pacific. During the decaying period of the WP-El Niño, anomalous high chlorophyll appears concurrently with anomalous low SST in the eastern Pacific. Conversely, anomalous high chlorophyll appears in the central Pacific prior to the decaying period of the CT-El Niño. In particular, the anomalous low sea level from the northwestern Pacific shifts to the southern equatorial region during the decaying period of the CT-El Niño. This drives anticyclonic boundary currents which enhance the Equatorial Undercurrent, playing a role in the supply of nutrients to the central equatorial Pacific, resulting in an increase in chlorophyll concentration in the same region.