Acid fracturing is a key stimulation method for deep and ultra-deep carbonate reservoirs, where extreme temperature-stress conditions and pervasive natural fractures frequently compromise treatment effectiveness. Natural fractures act as competing flow pathways that divert and consume acid, reducing etching efficiency and limiting fracture conductivity. To address this challenge, this study establishes a geology-engineering integrated framework that links multi-scale fracture characterization with high-temperature (150 °C), high-stress (0 to 80 MPa) acidizing experiments. Geological characterization, combining 2D petrography and 3D fracture reconstruction, reveals abundant high-angle fractures with variable mineral fillings (quartz, calcite, and clay). Based on their distinct physicochemical reactivity with acid, natural fractures are classified into three engineering-relevant types: reactive-filled fractures (RFF), inert-filled fractures (IFF), and open-conduit fractures (OCF). Correspondingly, acid transport exhibits three interference modes: deflection (RFF; controlled by coupled acid–carbonate reaction and gas effects), obstruction (IFF; dominated by siliceous mechanical blocking), and bifurcation (OCF; controlled by physical leak-off). Experimental results demonstrate that etch-induced mass loss follows OCF > IFF > RFF, whereas effective acid penetration distance follows the reverse trend (RFF > IFF > OCF), indicating that high acid consumption does not equate to effective utilization. Dolomite samples develop higher surface roughness (JRC) and show stronger sensitivity of conductivity to fracture filling type, while limestone exhibits uniformly low JRC and conductivity due to its more homogeneous dissolution. These findings clarify the mechanistic role of natural fracture fillings in acid transport and fracture conductivity and provide a quantitative basis for designing acid fracturing treatments in fractured deep and ultra-deep carbonate reservoirs.