2,2′,4,4′-Tetrabromodiphenyl ether (BDE-47) is a persistent organic pollutant that spreads widely in the marine environment. Our previous studies found that it had adverse effects on the marine algae and caused a series of stress responses. This present study used BDE-47 as a stress, which has high biotoxicity. Firstly, 9 species of microalgae from different phyla were targeted to observe and prove the prevalence of apoptosis and autophagy in marine microalgae under BDE-47 stress, and then apoptosis, autophagy and their interactions were systematically investigated by taking the more stress-sensitive alga. On this basis, the effects of apoptosis and autophagy on interspecific competition of microalgae were discussed. The main research results obtained are as follows: (1) BDE-47 was a highly toxic substance with obvious acute toxicity to marine microalgae, and apoptosis and autophagy occurred in different species of microalgae under the stress of BDE-47, which is universal. (2) BDE-47 induced apoptosis through the mitochondrial apoptosis pathway and the death receptor apoptosis pathway, and at the same time induced autophagy through the three phases of autophagy initiation, membrane nucleation, and autophagosome prolongation. Autophagy and apoptosis were mutually regulated, and the two were in an antagonistic relationship. (3) BDE-47-induced oxidative stress in algal cells was the key trigger for activation of apoptosis and autophagy. Activated autophagy had the protective effect of alleviating oxidative stress. (4) A co-culture system of I. gaIsochrysis galbana and Platymonas helgolandica was established under experimental ecological conditions. Inhibiting autophagy further increased the competitive advantage of helgolandica in competition, whereas inhibiting apoptosis partially restored the competitive advantage of I. galbana in competition under BDE-47 stress,, suggesting that apoptosis and autophagy may be new pathways affecting interspecific competition among microalgae. This study will provide a new research perspective and research ideas for clarifying the environmental mechanism of coastal pollutants and revealing the reasons for their impact on the community structure of microalgae.