In distributed implementations of memory-bound stencil AMR applications, the inter-node communication time often represents a major performance bottleneck. Thus minimizing communication is an objective as important as maintaining a good load balance. We propose a new domain partitioning method for block-based AMR applications based on the multi-phase-field (MPF) model. The MPF model for polycrystalline growth minimizes the interfacial energy and forms a convex shape for each crystal grain. In our method, each phase of the MPF model represents a computational sub-domain of each MPI process. We apply the proposed partitioning method to a block-based AMR application for an interface capturing on multiple GPUs. We measured the strong scalability up to 256 GPUs on the TSUBAME3.0 supercomputer at Tokyo Institute of Technology. The proposed MPF partitioning can successfully improve the strong scalability and reduce the communication cost of a block-based stencil AMR application.