A kind of tracking error of shipboard electro- optical tracking system is caused by the rotation of vessel. In order to solve this problem, a method using coordinate transformation based on quaternion is proposed. By analyzing the viewing field in each coordinate system, the effect of vessel attitude on the viewing field is deduced. Meanwhile, the effect of the installation misalignment on the viewing field is deduced too. The result provides a theoretical basis for real-time despinning of shipboard electro-optical tracking system.