The toxic effects of 2,2′,4,4′-tetrabromodiphenyl ether (BDE-47) on the marine alga Skeletonema costatum were studied, including the population dynamics, chlorophyll fluorescence characteristics, pigment content, superoxide dismutase (SOD) activity, malondialdehyde (MDA) content and morphology. High doses (200–600 μg L−1) of BDE-47 significantly suppressed the population growth of S. costatum, with a 96 h EC50 value of 293 μg L−1. Photosynthetic parameters (Fv/Fm, rETRmax and ΦPSⅡ) of photosystem II (PSII) were significantly inhibited with increasing BDE-47 concentrations. The chlorophyll c (chl c) concentration was also inhibited by exposure to BDE-47. In contrast, chl a and carotenoid concentrations were elevated after exposure to high concentrations of BDE-47 for 72 and 96 h. The SOD activity was generally higher at concentrations of 100–600 μg L−1 than those of the control when the exposure time was less than 48 h. With increasing time, the SOD activity generally decreased, and significantly higher SOD activity only occurred in the treatment with high doses of BDE-47. High MDA contents occurred after exposure for 96 h in all BDE-47 treatments. With increasing BDE-47 concentrations, drastic deformation of the silicious valve and detachment of the strutted processes were found. In addition, drastic decreases in the BDE-47 concentration in culture medium indicated the bioaccumulation of BDE-47 by S. costatum. Our results revealed multiple responses of S. costatum to BDE-47 exposure, and indicated the potential risk of BDE-47 in the East China Sea based on these responses.