In the long-term deep burial process of high-level radioactive waste, the flow of gas generated within the disposal facility through the buffer zone of bentonite material is recognized as a significant factor affecting the long-term safety and stability of the repository. A critical understanding of gas migration and breakthrough patterns is thereby established. To facilitate an in-depth study of this phenomenon, a compacted saturated Gaomiaozi (GMZ) bentonite sample with a dry density of 1.7 g/cm³ was selected for pore structure analysis and numerical simulation of gas breakthrough. Three-dimensional pore structure models were generated and validated utilizing pore characteristic parameters obtained from mercury intrusion porosimetry, alongside Gaussian random field two-phase theory, superposition theory, and mathematical morphology image processing methods. Following this, numerical simulations of gas migration and breakthrough processes were conducted, resulting in the acquisition of parameters such as breakthrough path length, tortuosity, and breakthrough throat size. Gas breakthrough pressure was calculated using the Young-Laplace equation. The results indicate that the tortuosity of the seepage paths within the bentonite model ranges from 1.98 to 3.72, characterized by a complex pore network morphology and multiple meandering gas migration pathways. It is found that the breakthrough throat sizes range from 0.024 μm to 0.04 μm, leading to calculated gas breakthrough pressures between 7.20 MPa and 12.00 MPa, which closely align with the experimental values reported in the literature. This further validates that capillary-driven gas-liquid two-phase flow is established as the dominant mode of gas migration in compacted saturated GMZ bentonite.