Acid fracturing technique is widely applied to stimulate the productivity of carbonate reservoirs. The acid-fracture conductivity is created by non-uniform acid etching on fracture surfaces. Heterogeneous mineral distribution of carbonate reservoirs can lead to non-uniform acid etching during acid fracturing treatments. In addition, the non-uniform acid etching can be enhanced by the viscous fingering mechanism. For low-perm carbonate reservoirs, by multi-stage alternating injection of a low-viscosity acid and a high-viscosity polymer pad fluid during acid fracturing, the acid tends to form viscous fingers and etch fracture surfaces non-uniformly. To accurately predict the acid-fracture conductivity, this paper developed a 3D acid fracturing model to compute the rough acid fracture geometry induced by multi-stage alternating injection of pad and acid fluids. Based on the developed numerical simulator, we investigated the effects of viscous fingering, perforation design and stage period on the acid etching process. Compared with single-stage acid injection, multi-stage alternating injection of pad and acid fluids leads to narrower and longer acid-etched channels.