Due to climate change and human activities, seagrass is in crisis as the coverage of seagrass declines at an accelerated rate globally. In this paper, the severe challenges of seagrass ecosystem were briefly reviewed, including adverse effects of natural factors and human activities on seagrass beds. The research status of pollutants and pollution in seagrass bed ecosystem was reviewed, the future research directions in related fields were proposed as well. The eutrophication in coastal waters and discharge of pollutants such as sulfide, heavy metals, organic matter and microplastics caused by human activities are important reasons for seagrass loss. In addition, environmental stressors lead to reduced immunity and decreased resistance of seagrass to various pathogens, leading to seagrass wasting diseases. Future studies concerning the influence of novel pollutants, i.e., plastic waste on non-native algae, microorganisms and seagrasses, as well as their interrelationships, will be of vital importance. In addition, researches on seagrass wasting diseases and their pathogens should be much accounted in China, to fill in gaps in related fields and improve the response ability to emergent seagrass diseases. In conclusion, this review was proposed to arouse the concern about the seagrass bed pollution, and provide possible enlightening information for the protection and restoration of this significant ecosystem.