Coal seam water injection is a key technology for achieving the co-mining of coal and coalbed methane. In response to the unclear mechanism of bubble migration in meso fissures that currently dominate the displacement of coalbed methane, this paper proposes a numerical simulation method based on CT images for exploring the migration mechanism of gas bubbles in the meso fissures of coal water injection. The meso fissure geometric modeling of coal water injection was reconstructed using CT scanning image analysis technology. Based on level-set theory, a bubble migration model under a two-phase fluid environment was constructed, and the influence characteristics of different fissure structures on bubble migration were explored. Furthermore, the mechanism of gas bubble migration within the meso fissures of coal water injection was revealed. Results show that the shape of the bubble with a radius of 0.03 mm oscillates obviously in the fissure structure with a length–width ratio of 1.3. The smaller the fissure structure diameter is, the larger the structure length–width ratio is, and the easier the bubble is to form gas resistance. Meanwhile, the larger the curvature of the fissure structure, the greater the contact angle between the bubble and the wall, and the easier it is for the bubble to detach from the wall. During the migration process, the size of the bubble constantly changes. With the increasing length–width ratio and width of the fissure structure, the equivalent radius of the bubble initially increases and then decreases. A negative correlation function is observed between bubble size and flow velocity. At low flow velocity, the volume of the bubble can increase by 18.17 %, and as the flow velocity increases, the volume of bubble can decrease by 54.53 %. In the bubbles aggregation process, an exponential function relationship can be observed between the bubble leading edge position and the bubbles spacing with a negative correlation. The influence of fissure structure on the bubbles is less than the interaction among bubbles. These results provide a theoretical basis for the efficient and increased extraction of coalbed methane.