Banana plantations are important tropical agro-ecosystems, and quantifying their greenhouse gas emissions is essential for developing low-carbon agriculture and mitigating global warming. The carbon balance of two banana cultivars (Musa paradisiaca AA (MA) and M. AAA Cavendish var. Brazil (MB)) was evaluated using the life cycle assessment (LCA) approach, based on field trials and farmer surveys in Chengmai County, Hainan Province, China. The results indicated that (1) both cultivation systems functioned as net carbon sinks, and the MB cultivar demonstrated a superior carbon balance, with a net sequestration of 21,652.88 kg CO₂ eq·ha⁻¹, significantly higher than the MA cultivar (15,197.96 kg CO₂ eq·ha⁻¹); (2) fertilizer management was the dominant source of anthropogenic emissions, contributing 74.03–81.76% of the carbon footprint from agricultural inputs; and (3) the MB cultivar’s enhanced carbon fixation capacity outweighed its higher emissions, resulting in a more favorable carbon balance than the MA cultivar. Concurrently, the banana plantations significantly increased soil carbon sequestration by 13.47–24.48%. Thus, within the studied system boundary, banana agro-ecosystems serve as net carbon sinks, a function that can be enhanced by optimizing fertilizer management to reduce emissions and by increasing both plant biomass and soil carbon sequestration. These results provide a scientific basis for low-carbon practices and promoting a more sustainable banana industry.