This paper investigates the registration decision of choosing national flag or flag of convenience (FOC) in the viewpoints of shipowers in Taiwan. A binary logit model is applied to analyze the important factors that influence the registration decisions. An empirical analysis based on a binary logit model about the shipowners’ choosing flags is conducted to demonstrate the conception developed in this paper. The results show that the registration decision is highly affected by the cost of seafarers, Hull & Machinery Insurance as well as maintenance and repair costs. Ship size also affects the registration decision, especially the larger the ship, the lower the utility is conducted by FOC. There are also differences between the preferences of deploying mainland China, sailing international services as well as operating container. In addition, reducing 20% of cost of seafarers will most affect the choice of vessel registry in four assumed scenes.