The Strait Exchange Foundation (SEF) and Association for Relations across the Taiwan Straits (ARATS) held the Second Chiang-Chen Meeting on November, 2008. The signing of the Cross-Strait Sea Transport Agreement between the SEF and ARATS has achieved a total direct shipping link across the Straits. In order to realize the actual situation of the negotiation and the problems caused by the Agreement, this study explores the Agreement and analyzes the negotiation through a structural approach. It is expected that the finding and results of this paper shall provide a reference for the following negotiations across the Straits.