In this article, investigations of the dynamic behaviors of a single bubble flowing across a mesh-based structure domain was conducted using the volume of fluid (VOF) model. The study was investigated in various mesh structure sizes, including hole size and gap distance. The fundamental behavior of bubble deformation and the effects of gap sizes were analyzed. Subsequently, the predicted dynamics of the deforming bubble area and the effect of the surface tension were examined inside the mesh holes. The discharging bubbles from the mesh structure resulted in a slight difference in the physical features from the original bubble dynamics before entering the mesh (flow restriction). This drafted the bubbles in different trajectories and led to behave differently based on the mesh characteristics. The complex interactions and the subsequent deformations were observed between different mesh sizes. For the validation of the bubble dynamics, the results of computational fluid dynamics (CFD) simulation were tested under different mesh sizes detailing the velocity field, exiting trajectory, bubbles deformation, and residence time, which helps to reveal the affected parameters on the separation mechanism of the original bubble.