The impact of the Fourth Industrial Revolution has brought significant attention to Condition-based maintenance (CBM) for autonomous ships. This study aims to apply CBM to the fuel supply pump of a ship. Five major failures were identified through reliability analysis, and structural analysis was conducted to investigate the mechanisms by which one failure induces another, leading to the identification of three compound failure scenarios. Data were collected on a test bed under normal conditions, five single failure conditions, and three compound failure conditions. The acceleration data from the experiments were transformed into 2D arrays corresponding to a single pump rotation, and a method was proposed to compensate for the errors accumulated during the repeated array generation. The data were vectorized using a simplified CNN structure and applied to six multi-label learning methods, which were compared to identify the optimal approach. Among the six methods, the Label Powerset (LP) was found to be the most effective. Multi-label learning captures correlations between labels, similar to the failure-inducing mechanisms learned from structural analysis.