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Evaluating ship encounters probability efficiently is significant for maritime transportation risk analysis as well as improving maritime traffic safety. In practice, ship encounters probability estimate by using traditional observation or field experiments is nearly impossible due to the expensive cost. In this paper, we propose a methodology framework for evaluating ship encounters probability based on an agent-based simulation paradigm. Individual ship’s navigation behavior is modeled as an agent, and their encounters are detected by an innovative geographic information system (GIS)-based intelligent algorithm. We then design and implement a prototype simulator based on the methodology framework and apply it in the mid-western waters of Bohai Sea of China to demonstrate its functionalities and utility. The findings show that the framework proposed in this paper has potential to provide decision support for guiding future marine transportation planning. This paper offers new insights and valuable demonstration on promoting maritime traffic safety management with the integration of GIS and emerging complex system simulation technology.