Algae and bacteria play important roles in the biogeochemical cycle, energy flows of important elements in the ecosystem. Some bacteria can have beneficial interactions with algae by promoting the growth of algae and helping algae resist stress, thereby having important impacts on the survival, competition, and physiological functions of both partners. This article reviewed the main ways of interaction, microbial communities, molecular mechanisms, and the recent applications of beneficial interactions between algae and bacteria in the treatment of environmental pollution, biomass energy, and synthetic biology to in-depth study the beneficial interactions between algae and bacteria. The studies on the beneficial interactions between algae and bacteria were prospected. It will not only play an important role in understanding the structure and function of microbial community in aquatic environments, and the mechanisms and effects of relationships among microbial species, but also provide important scientific basis for maintaining the health of ecosystems, mining and utilizing the biological resources for the benefit of humanity.