The gas and water flow behavior in rough-walled hydrophilic fractures at the pore scale is crucial for understanding the gas production characteristics of naturally fractured formations. This paper presents a systematic analysis of the gas and water flow characteristics in both the single-fracture and Y-shaped junction fracture models using the volume of fluid (VOF) method. Numerical simulations showed that the gas/water rate ratio is the most significant factor influencing gas bubble/slug geometry, phase distribution, and saturation. The effect of fracture roughness and tortuosity is less significant than the gas/water ratio, whereas the total fluid rate has a negligible effect. For Y-shaped junction models, the phase distribution and referential pathways are predominantly controlled only by the channel aperture ratio, whereas the effect of the intersecting angle and fluid flow rate can be neglected.