Climate warming has a significant impact on the sea ice and ecosystem of the Arctic Ocean. Under the increasing numbers of melt ponds in Arctic sea ice, the phytoplankton communities associated with the ice system are changing. During the 7th Chinese National Arctic Research Expedition cruise in summer 2016, photosynthesis pigments and nutrients were analyzed, revealing differences in phytoplankton communities between melt ponds and open water in the central Arctic. Photosynthetic pigment analysis suggested that Fuco (5–91 μg m −3) and Diadino (4–21 μg m −3) were the main pigments in the open water. However, the melt ponds had high concentrations of Viola (7–30 μg m −3), Lut (4–59 μg m −3) and Chl b (11–38 μg m −3), suggesting that green algae dominated phytoplankton communities in the melt ponds. The significant differences in phytoplankton communities between melt ponds and open water might be due to the salinity difference. Moreover, green algae may play a more important role in Arctic sea ice ecosystems with the expected growing number of melt ponds in the central Arctic Ocean.