The influences of El Niño on the changes of sea surface temperature (SST) and chlorophyll have been well studied, but its impact on changes of particulate organic carbon (POC) remains unclear. In this study, we analyzed the time series of POC and found that from January 2003 to December 2011, the spatially-averaged POC increased at a rate of 0.24 mg/m3 per year. However, during the 2009–2010 El Niño, the spatially-averaged POC increased at a rate of 1.78 mg/m3 per month. This indicated that the increase of POC during 2009–2010 may be related to El Niño. To investigate the relationship between POC and El Niño, we introduced the phase shift time between the POC and the Multivariate ENSO Index (MEI) to characterize the response of POC to El Niño, and calculated the correlation between the time series of the MEI and POC anomalies during El Niño to determine the phase shift time. The results of cross-correlation analysis indicated that changes of POC were delayed from the onset of El Niño by 4 months. Furthermore, a detailed analysis was presented based on a range of in situ observations and satellite-derived datasets available during the 2009–2010 El Niño. The correlation coefficients between POC and chlorophyll, as well as between POC and SST, are 0.9263 and −0.8315, respectively, and the constructed model indicated that chlorophyll and SST had a significant impact on POC. The spatial distribution of POC anomaly maximum occurred in the spring of 2010, because in the winter of 2009, the Rossby-type anomalies were reflected as upwelling Kelvin wave. However, the vertical POC anomaly maximum occurred in the spring of 2011, because the 2009–2010 El Niño experienced a fast phase transition from warm El Niño to cold La Niña, which was associated with oceanic upwelling.