The modeling and design of multi-agent systems is imperative for applications in the evolving intelligence of unmanned systems. In this paper, we propose a multi-agent system design that is used to build a system for training a team of unmanned surface vehicles (USVs) where no historical data concerning the behavior is available. In this approach, agents are built as the physical controller of each USV and their cooperative decisions used for the USVs’ group coordination. To make our multi-agent system intelligently coordinate USVs, we built a multi-agent-based learning system. First, an agent-based data collection platform is deployed to gather competition data from agents’ observation for on-line learning tasks. Second, we design a genetic-based fuzzy rule training algorithm that is capable of optimizing agents’ coordination decisions in an accumulated manner. The simulation results of this study demonstrate that our proposed training approach is feasible and able to converge to a stable action selection policy towards efficient multi-USVs’ cooperative decision making.