Abstract: The biological pump is one of the main pathway of carbon sequestration in marine ecosystems. Much progress has been made in the study of biological pump in both open ocean and marginal sea ecosystems in the past 3 decades since the implement of the JGOFS program. This review addresses the progress on the study of biological pump, focusing on the influence of phytoplankton and zooplankton community structures, and update knowledge on the influence of warming and ocean acidification on biological pump under the global climate changes. The review finally makes a few suggestions for future research directions, including further study on the biological pump in contrasting marginal sea ecosystems, the biological processes in the twilight zone, as well as the response to global changes. Application of new protocols and development of more reliable model were also suggested.