The invention relates to a pumping stop sand setting fracture-height-controlling acid fracturing process method applicable to a carbonate reservoir. The method comprises the following work procedures that before the normal fracturing, low-viscosity slickwater is adopted for fracture making, and the initial fracture height is controlled; then, after the slickwater enters the stratum in a way of carrying support agent sand, the pumping stop is adopted for prompting the support agent sand to be settled near a fracture opening, so that each stage of support agent sand shields the back section in advance, a high-intensity artificial separation layer is formed, the stress state is changed, and the goal of effectively controlling the lower fracture height extending to prevent the communication with the lower part water body is achieved; low-viscosity fracturing fluid is injected for fracture making at a stable discharge capacity; after the fracturing fluid enters the stratum, acid liquid is injected for etching the stratum, and high-flow-guide capability artificial fractures are formed; after the acid liquid is extruded into the stratum, the pumping is stopped for measuring the pressure drop, and the construction is completed. The process has the advantages that the artificial separation layer can be formed, the fracture height vertical direction extending can be controlled, the stress state is changed, and the goals of effectively controlling the lower fracture height extending and preventing the communication with the lower part water body are achieved.