Carbon capture through biological CO2 fixation can help to reduce the global warming potential. The use of algae systems has been identified as the most efficient and economical approach for CO2 fixation and has been realized by many developing and developed countries. However, low biomass productivity and harvesting costs limit its scale-up. To break through this technical barrier, it is necessary to study the efficiency of photosynthetic carbon sequestration in marine ecosystems, which reduced production costs significantly. In this chapter, the biological characteristics of marine algae and the principles and challenges are presented; the carbon sequestration factors of marine algae are summarized, and specific ways to improve the carbon sequestration efficiency of marine algae are proposed; subsequently, the physiological mechanisms of carbon sequestration in marine microalgae (especially carbon-concentrating mechanisms) are presented and recent advances are described, and the limitations of carbon sequestration in marine microalgae are presented. The interdisciplinary significance of the carbon sequestration efficiency of marine microalgae is further examined, and the carbon sequestration efficiency of marine microalgae is reconstructed.