The Western Pacific Ocean (WPO) is one of the most active eddy regions in the world, where a variety of ocean processes are frequently observed, but little research has been conducted on the phytoplankton communities and their photosynthetic physiological status within the eddies in this region. The bio-optical parameters of phytoplankton communities and their physiological status within the warm core and cold core eddies of the WPO during the winter of 2021 were investigated based on fast repetition rate fluorometry (FRRF). In this paper, environmental factors, phytoplankton community parameters, chlorophyll a (Chl a), and various bio-optical parameters were investigated for two opposite types of eddies at the WPO. The results show the maximum [Fv/Fm, 0.18 to 0.26 (warm eddy), 0.14 to 0.28 (cold eddy)] and effective photosynthetic efficiency [Fq'/Fm', 0.11 to 0.23 (warm eddy), 0.10 to 0.27 (cold eddy)] of the DCM for both warm and cold eddies, the electron transport rates ETRRCII [0.002–6.18 mol e− mol RCII−1 s−1 (warm eddy), 0.002–4.94 mol e− mol RCII−1 s−1 (cold eddy)] and the primary production potential PPmax [0.68–118.19 mg C (mg Chl a)−1 day−1 (warm eddy), 2.47–243.49 mg C (mg Chl a)−1 day−1 (cold eddy)] for different types eddies. In warm eddy, temperature and Chl a concentrations had significant effects on Fv/Fm and Fq'/Fm', while in cold eddy the correlation of Fv/Fm and Fq'/Fm' with temperature was not significant, and Fv/Fm was significantly negatively correlated with DIP only. Light was the main variable affecting the electron transport capacity and primary production potential of the phytoplankton community in the eddies, while larger cyanobacteria and dinoflagellates contributed significantly to the primary production potential of the cold eddy. In addition, both eddies centers had higher primary production potentials, with the cold eddy had a higher primary production potential than the warm eddy, based on microscopic analysis this phenomenon may be due to differences in electron transfer rates between phytoplankton communities.