We analyzed the three-dimensional distribution of micropores and internal structures in both fresh and weathered granite using micro-focus X-ray computed tomography (micro-CT). Results show that the pore radius in fresh granite is mostly in the range of $17-50{mu}m$, the throat radius is in the range of $5-25{mu}m$, and the coordination number (CN) of pores is less than 10. In contrast, the pore radius in weathered granite is mostly in the range of $20-80{mu}m$, the throat radius is in the range of $8-30{mu}m$, and the CN is less than 12. In general, a positive linear relationship exists between pore radius and CN. In addition, both the size and the density of pores increase with an increasing degree of rock weathering. The size of the throats that connect the pores also increases with an increasing degree of weathering, which induces fracture propagation in rocks. Micro-CT is a powerful and versatile approach for investigating the three-dimensional distributions of pores and fracture structures in rocks, and for quantitatively assessing the degree of pore connectivity.