There are also obvious inter-annual variations of the North Equatorial Countercurrent (NECC) during the occurrence and development of the El Niño-Southern Oscillation (ENSO), but its changing process in hydroecological conditions and response mechanism influenced by ENSO cycle are still unclear. Taking the NECC affected area in the tropical western Pacific as the study area, this paper analyzes the characteristics of the changes of hydroecoclimatic conditions at different stages during the ENSO cycle during autumn and winter transition period from 2006 to 2022. Results reveal that there are high chlorophyll concentration bands in the NECC source area and its path, which are formed by the combined influence of nutrients carried by the NECC from its source area and the New Guinea Coastal Undercurrent. The upwelling of the Mindanao Dome also has a great influence on the nutrient supply. When El Niño events occurred, the westerly wind events in the tropical western Pacific increased, the NECC strengthened, a large amount of surface water moved eastward, the sea level in the study area decreased, the deep water recharge to the shallow layer increased, and the deep cold water rose. The jointly enhanced NECC, New Guinea Coastal Current, New Guinea Coastal Undercurrent and Mindanao Dome upwelling transport more nutrients to the sea surface from both horizontal and vertical levels, resulting in significant increases in surface chlorophyll concentration and primary organic carbon production by all types of phytoplankton. When La Niña events occurred, the changes of ecohydroclimatic conditions in the NECC affected area are almost opposite to those during El Niño events, but the degree of change is weaker than that during El Nino events. The combined weakening of the NECC, the New Guinea Coastal Undercurrent and the Mindanao Dome upwelling significantly reduce the nutrients delivered to the sea surface from the horizontal and vertical levels. The chlorophyll concentration and primary organic carbon production by all types of phytoplankton decreased significantly. This paper proposes a model of the response mechanism of the evolution of hydroecoclimatic conditions in the NECC affected area to El Niño and La Niña events, which is conducive to further analysis of the role of ENSO cycle in local ecological effects and hydroclimatic evolution. It has important significance for understanding the impact of global climate change on the material cycle.