Copepods play important roles in maintaining the structure of marine ecosystem due to their key position in food chain and their numerous species, quantities and wide distribution. The nutrients obtained by copepod larvae can directly affect their development, then the complement of adult copepods and even their population stability. In this study, in situ feeding of copepodites was evaluated by molecular methods in the waters near the nuclear power plant in Daya Bay (S1: control station, S2: outfall station) in summer 2015. The results showed that 16 prey species in total were identified in both stations, including diatoms (11 species), tunicate (two species), fungi (one species), ichthyosporea (one species), and oomycetes (one species). Diatoms (47.30%) and tunicate (41.89%) were the most abundant food types revealed by the significant proportion of the clones. Similar feeding diversity was discovered in copepodites at S1 and S2, with nine prey species at S1 and 10 at S2, but significant differences in diet composition were revealed, with metazoan (61.54%) and diatoms (68.57%) dominating the diets of copepodites at S1 and S2, respectively. In addition, copepodites appeared to be more herbivorous at S2 with a lower Omnivory Index (0.31) than at S1 (0.72). These results suggested that copepodites could optimize their diet composition by consuming a reasonable percentage of animal and plant materials according to available food sources. More phytoplankton, especially diatoms as diet of copepodites at the outfall station implied that copepodites might change their feeding habits with global warming development.