With the increasing severity of marine pollution, the living space of more and more marine organisms is threatened. Due to the persistence and bioaccumulation of pollutants, these artificially generated compounds will return to human society through the food chain pathway. This chapter provides an overview of the pollution of emerging pollutants (EPs) pesticides, brominated flame retardants (BFRs), perfluorinated compounds (PFCs), pharmaceuticals and personal care products (PPCPs), and microplastics (MPs) on marine ecosystems and their toxicity on organisms. We found that these EPs are distributed in multiple maritime spaces. Due to human activities and the discharge of urban sewage, pollutants are enriched in surface water and sediment near estuaries and coasts and exhibit spatial distribution differences. These EPs are mostly lipophilic substances that can accumulate in marine organisms and cause oxidative stress, inflammatory response, cell apoptosis, and enzyme dysregulation by interfering with key signaling pathways and gene expression. EPs cause endocrine, immune, metabolic, and physiological dysfunction, which leads to neurotoxicity, reproductive toxicity, and developmental toxicity. It is urgent to confront the threat of EPs to marine ecosystems. We hope this chapter can provide theoretical and data support for the prevention and toxicity research of pollutants.