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This paper presents the development and implementation of a scheduling method that enables the BSA Autonomous Underwater Vehicle (AUV) to perform a mission operation while managing various resources autonomously. The mission is to survey several local areas in a dynamic ocean environment with different survey sensors. When a mission begins, it is assumed that during the execution of the mission, there is no communication between the vehicle and operator, the vehicle is then completely autonomous until the mission finished. So, an on-board scheduling is development to supervise, manage and control the implementation of the mission. It behaves like a soft real-time system and is realized by discrete events driven hierarchical Petri Net (PN). The highest level PN and lower sub-PNs with designed events are introduced detailedly. The feasibility and effectiveness of the mission scheduling is checked by lake trials in nominal and degraded situations.