Acid fracturing is essential in enhancing recovery efficiency, especially within carbonate reservoirs. Although extensive studies have been conducted on hydraulic fracturing, understanding the intricate dynamics between acid–rock reactions and fracture propagation in heterogeneous layered reservoirs remains limited. This study employs a comprehensive coupled hydro-mechanical-chemical flow framework to investigate acid fracturing processes in layered geological formations. The model incorporates a two-stage homogenization approach to account for rock heterogeneity, a dual-scale continuum framework for fluid flow and acid transport, and a phase field method for examining fracture propagation. We thoroughly examine how treatment parameters, particularly acid concentration and injection rate, affect fracture propagation modes. The analysis identifies three distinct propagation patterns: crossing, diversion, and arresting. These are influenced by the interplay between pressure buildup and wormhole formation. Initially, higher acid concentration aids in fracture crossing by lowering the peak pressure required for initiation, but excessive concentration results in arresting because it causes extensive wormhole development, which reduces fluid pressure. Similarly, the injection rate plays a crucial role in fracture movement across layer interfaces, with moderate rates optimizing propagation by balancing pressure and wormhole growth. This comprehensive modeling framework serves as a valuable prediction and control tool for acid fracture behavior in complex layered formations.