Aquaculture is an important part of aquaculture, and its greenhouse gas emissions cannot be ignored. In order to clarify the calculating methods, flux measurement, and influencing factors of carbon emissions in aquaculture ecosystems, this paper systematically reviewed and integrated relevant research on greenhouse gas emissions of aquaculture, summarized the current calculation methods of greenhouse gas emissions, including oak ridge national laboratory method, Intergovernmental Panel on Climate Change emission factor method, and life cycle assessment method, and outlined methods for measuring greenhouse gas emissions, such as inverted funnel method, eddy covariance technique, and static chamber method. In addition, this paper analyzed various factors affecting greenhouse gas emissions from the perspectives of aquaculture species, water management mode, temperature, and feed. The study found that: ① greenhouse gas emission calculating methods have not reached a consensus in the present scientific community, the calculation formulas are oversimplified, and the factors considered are not comprehensive; ② flux measurement is complex, and the measurement accuracy and efficiency need to be improved; ③ there are many factors that affect carbon emissions, and feed is the largest contributing factor to greenhouse gas emissions from quaculture, but limited studies have addressed the aquatic animal-derived metabolic carbon generated by feeding. This paper points out that relevant research currently has certain limitations, and proposes suggestions for future research on greenhouse gas emissions of aquaculture from four angles: estimation methods, factors considered, monitoring time, and N₂O emission factors, in order to provide inspiration and assistance for deeper research in the future.