Characterization of rock permeability change during the fracture network evolution is critical to the design and assessment of geological storage facilities. Under geo-storage conditions, rock fractures propagate during damage processes and re-bond during healing. However, natural heterogeneities in rocks significantly reduce experimental repeatability. Moreover, healing is a time-consuming process and requires high pressure or temperature to achieve. In this study, we resort to the 3D printing technology for specimen preparation so that complex rock microstructure changes are precisely controlled. We validate the specimen preparation by comparing experimental permeability test results with analytical solutions. Channel networks with different tortuosity, porosity, fracture branch, and structural anisotropy are designed to mimic various microstructure changes in rocks. To fabricate fractured rocks, we also embed heterogeneous fracture networks into 3D printed specimen and modify fracture geometry to account for anisotropic microstructural changes. Experimental findings revealed the evolution trend of permeability with these structural characterization parameters. They also match well with those obtained from computational fractured rock models under identical hydro-mechanically coupled conditions. This study is expected to provide new insights into the dependence of rock permeability on its microstructures under complex geo-storage conditions.