In this study, we conducted a quantitative analysis of the behavior of ascending methane bubbles, which were filmed at two natural gas seep sites and reproduced by numerical simulations using two-dimensional motion analysis software. The targeted sites were located in the southwest and northeast of Sado Island at the eastern margin of the Sea of Japan, where methane bubbles with and without a methane hydrate (MH) layer were observed, respectively. The simulations comprising gas bubbles and MH bubbles spouting from a nozzle in the computational domain filled with pure water were generated to assess the validity of the image analysis for situ-data, while the numerical models and physical properties were utilized for current two-phase (gas-liquid) simulations. The rising velocity, size, circumference, circularity, and maximum diameter of methane bubbles were examined to understand the effects of the MH layer on the statistical and stochastic features of ascending methane bubbles. Based on the statistics of the aforementioned variables, gas bubbles had a higher rising velocity and smaller circularity than MH bubbles when the bubble sizes were identical. Furthermore, the stochastic analysis indicated that the circularity of the MH bubble was uniquely determined by the size of the bubble owing to the more rigid skin of the MH bubbles compared to that of the gas bubbles.