The Atomic Kinetic Monte Carlo (AKMC) method provides insights into the macroscopic behavior of materials through atomistic-level simulations and finds broad applications in materials science innovation. Improving simulation scale and performance remains a consistent focus in the development of parallel AKMC software. We port the AKMC software to GPU clusters. To alleviate the memory pressure in large-scale complex system simulations, we redesign the data layout and propose the Lattice Data Compression and Vacancy Data Decompression algorithms. Additionally, We propose a multi-level pipeline scheme combined with an on-demand communication forwarding and merging strategy to reduce data transfer and communication overhead. Compared to state-of-the-art KMC software, MISA-AKMC achieves a 10.41-fold improvement in computational throughput and a 52.07-fold expansion in simulation scale. We implement the first true micrometer-scale AKMC simulation involving 20 quadrillion atoms on GPU clusters. MISA-AKMC achieves 96.03% parallel efficiency in weak scaling and 85.29% in strong scaling on 16,000 GPUs.