For ultra-deep carbonate rock reservoirs with poor pore connectivity, acidification is required to communicate reservoir space and enhance productivity. The high temperatures in ultra-deep reservoirs lead to fast reaction rates between acid and rock, resulting in short acid-etched fissures post-acid-fracturing. However, effective non-uniform etching cannot be achieved, causing a sharp decline in flow capacity after modification. To address the challenges of ultra-deep carbonate rock modification, the paper conducted multi-level alternating acid injection simulation experiments. Based on the Reynolds similarity criterion, experimental parameters were optimized by adjusting engineering parameters to study rock etching morphology and fissure flow capacity under various alternating series. The research results indicate that the non-uniform etching of rocks is most pronounced after simulating three levels of alternating etching, with significant etching grooves on the rock surface. Scanning the rock core surface for elevation fluctuations and roughness reflecting the elevation fluctuations and roughness of alternating etched fissures showed that the undulation and roughness of the three-level alternating acid-etched fissure contours were the greatest. Test data on fissure flow capacity validated that rocks exhibit the best flow capacity after three-level alternating etching. The application of the optimized three-level alternating acid fracturing process in ultra-deep acid fracturing demonstrated improved productivity, offering effective technical support for ultra-deep reservoir modifications.