Abstract: Agriculture has played a vital role in the development of the national economy and social stability. However, there is ever-increasing pressure on agricultural production, due to the rapid growth of population and urbanization. Chemical fertilizers, antibiotics, and feeds have also been widely used to cause serious pollution in large-scale production. Furthermore, the competition between humans and animals for grain resources (such as corn and soybeans) has increasingly come to the forefront under the rapid advancements in the livestock and poultry industry. Additionally, the fish meal can serve as a vital component in the protein and essential nutrients in aquatic feeds. Yet some challenges have posed sufficient production and safety concerns in aquaculture. Thus, new technologies are very necessary to support sustainable agriculture. Among them, microalgae have been widely used to assimilate pollutants (such as nitrogen and phosphorus), as well as contain some nutrients and bioactive substances that promote the growth of animals and plants, and the quality of agricultural products. This review aims to first summarize the current applications of microalgae and its biochar in the planting industry. Some nutrients were slowly released to enhance the physical and chemical properties of the soil, thus facilitating plant growth. Additionally, the bioactive substances derived from microalgae were used to mitigate the threats from the biotic and abiotic factors to crops, which was also used to directly stimulate plant growth and metabolism. Secondly, the recent advancements were summarized on the microalgae for livestock wastewater treatment and feed additives. Both pollutant removal and nutrient recovery were effectively achieved by utilizing the microalgae in the treatment of livestock and poultry wastewater. However, further investigations were necessary to enhance the economic viability and practicality of microalgae-based livestock and poultry wastewater treatment. The efficiency of microalgae was also enhanced to remove the pollutants from undiluted livestock and poultry wastewater. Microalgae also served as an exceptional feed additive, providing a wealth of benefits for livestock and poultry. Abundant reserves were offered for the proteins, polysaccharides, dietary fibers, and vitamins. Microalgae were also incorporated into the diets of ruminant animals, pigs, and poultry, in order to enhance the immune systems, intestinal microbial communities, and ultimately growth. Moreover, the inclusion of microalgae as a feed additive also significantly promoted the nutritional value of their products in the livestock and poultry industry. This review also provided a comprehensive overview of the research progress on the application of microalgae in aquaculture. A similar role of microalgae was achieved in aquaculture and livestock and poultry industries. In terms of agriculture wastewater treatment, the combination of bacteria and microalgae (known as the bacterial-algal symbiotic system) showed great potential for future application. Furthermore, some techniques were required to detoxify the harmful microalgae, in order to reduce the bioaccumulation of pollutants in microalgae for the safety of microalgae feed additives. Additionally, it was very necessary to evaluate the toxic behaviors of wastewater and flue gas-cultured microalgae. Furthermore, the microalgae was applied to yield significant environmental and economic benefits, according to the life cycle assessment and techno-economic analysis. Future research should be given to optimize the cultivation mode of microalgae, in order to improve their efficiency in pollutant removal and harvesting cost saving. Moreover, it is also important to clarify the toxic effects of various pollutants on microalgae and their subsequent utilization. Additionally, systematic evaluations should be conducted on the economic viability and sustainability of microalgae in agricultural applications. The finding can also provide a theoretical basis for the large-scale application of microalgae in sustainable agriculture.