The amount of methane leaked from deep sea cold seeps is enormous and potentially affects the global warming,ocean acidification and global carbon cycle. It is of great significance to study the methane bubble movement and dissolution process in the water column and its output to the atmosphere. Methane bubbles produce strong acoustic impedance in water bodies, and bubble strings released from deep sea cold seeps are called gas flareswhich expressed as flame-like strong backscatter in the water column. We characterized the morphology and movement of methane bubbles released into the water using multibeam water column data at two cold seeps. The result shows that methane at site I reached 920 m water depth without passing through the top of the gas hydrate stability zone (GHSZ, 850 m), while methane bubbles at site II passed through the top of the GHSZ (597 m) and entered the non-GHSZ (above 550 m). By applying two methods on the multibeam data, the bubble rising velocity in the water column at sites I and II were estimated to be 9.6 cm/s and 24 cm/s, respectively. Bubble velocity is positively associated with water depth which is inferred to be resulted from decrease of bubble size during methane ascending in the water. Combined with numerical simulation, we concluded that formation of gas hydrate shells plays an important role in helping methane bubbles entering the upper water bodies, while other factors, including water depth, bubble velocity, initial kinetic energy and bubble size, also influence the bubble residence time in the water and the possibility of methane entering the atmosphere. We estimate that methane gas flux at these two sites is 0.4×106–87.6×106 mol/a which is extremely small compared to the total amount of methane in the ocean body, however, methane leakage might exert significant impact on the ocean acidification considering the widespread distributed cold seeps. In addition, although methane entering the atmosphere is not observed, further research is still needed to understand its potential impact on increasing methane concentration in the surface seawater and gas-water interface methane exchange rate, which consequently increase the greenhouse effect.