The macro and micro morphology of rock failure surfaces play crucial roles in determining the rock mechanical and seepage properties. The morphology of unloaded deep rock failure surfaces exhibits significant variability and complexity. Surface roughness is closely linked to both shear strength and crack seepage behavior. Understanding these morphology parameters is vital for comprehending the mechanical behavior and seepage characteristics of rock masses. In this study, three-dimensional optical scanning technology was employed to analyze the micromorphological properties of limestone and sandstone failure surfaces under varying stress conditions. Line and surface roughness characteristics of different rock failure surfaces were then determined. Our findings reveal a critical confining pressure value (12 MPa) that influences the damage features of Ordovician limestone failure surfaces. With increasing confining pressure, pore depth and crack formation connecting the pores also increase. Beyond the critical confining pressure, the mesoscopic roughness of the failure surface decreases, and the range of interval-distributed pore roughness diminishes. Additionally, we conducted a detailed investigation into the water conductivity properties of rocks under different stress states using Barton's joint roughness coefficient (JRC) index and rock fractal theory. The roughness features of rock failure surfaces were classified into three categories based on mesoscopic pore and crack undulation forms: straight, wavy, and jagged. We also observed significant confining pressure effects on limestone and sandstone, which exceeding the critical confining pressure led to increased water conductivity in both rocks, albeit through different mechanisms. While sandstone exhibits fissures running across it, limestone shows shear abrasion holes. Beyond the critical confining pressure, the rock failure surface becomes smoother, leading to decreased water flow blocking capacity. The fractal dimension of Ordovician limestone increases significantly under critical confining pressure, leading to a more complex mesoscopic crack extension route.