Subnanometer catalysts offer high noble metal utilization and superior performance for several reactions. However, understanding their structures and properties on an atomic scale under working conditions is challenging due to the large configurational space. Here, we introduce an efficient multiscale framework to predict their stability exposed to an adsorbate. The framework integrates a comprehensive toolset including density functional theory (DFT) calculations, cluster expansion, machine learning, and structure optimization. The end-to-end machine-learning workflow guides DFT data generation and enables significant computational acceleration. We demonstrate the approach for CO-adsorbed Pd n (n = 1− 55) clusters on CeO 2 (111). Simulation results reveal that CO can facilitate restructuring by stabilizing smaller planar structures and bilayer structures of specific intermediate sizes, consistent with experimental reports. Metal−support interactions, preferential CO adsorption, and metal nuclearity and structure control catalyst stability. The framework allows automatic discovery of stable catalyst structures and a systematic strategy to exploit properties in the subnanometer scale.