Chattonella spp. are known to produce large amounts of reactive oxygen species (ROS); however, little is known about the mechanisms involved in mitigating the intracellular accumulation of ROS. In this study, a time-series of biological responses in C. marina var. antiqua under different oxidative stress conditions, induced by adding H2O2 at the initial concentrations of 100 and 500 µM, was investigated. Although the added exogenous H2O2 was rapidly consumed at 3 h post-exposure (hpe), intracellular ROS levels were enhanced in the 500 µM H2O2 group but decreased in the 100 µM H2O2 group. Accompanied by increased intracellular ROS levels, the photosynthetic activity of C. marina var. antiqua was considerably inhibited in the 500 µM H2O2 group, but not in the 100 µM H2O2 group. The Fv/Fm ratio and PIABS were negatively correlated with the intracellular ROS level, while the ABS/RC, TR0/RC, and DI0/RC were positively correlated with the intracellular ROS level. Expression of the gene encoding 2-cysteine peroxiredoxin (2-Cys Prx) was up-regulated in 100 µM H2O2 group at 6 hpe, but was down-regulated in 100 µM H2O2 group at 3 and 6 hpe. A negative relationship between the 2-Cys Prx transcript levels and intracellular ROS levels was detected. Results of the 2-DE proteomic analysis confirmed that the 500 µM H2O2 treatment down-regulated the expression of 2-Cys Prx and induced more damage to photosynthetic abilities of C. marina var. antiqua.