With the development of the water transportation, the ship number grows quickly, and the vessel traffic flow becomes more and more complex. Vessel traffic flow is analyzed from the aspects of ship number and time-space characteristic and composition and other behavior characteristics of vessel traffic flow. And the influence factors of vessel traffic flow are analyzed according to the time-space characteristic and the composition of vessel traffic flow. Meanwhile, the principles of traffic organization are put forward according to the essence of water traffic accident. And then, the necessity of studying and the feasibility of application on vessel traffic flow behavior characteristics are elaborated based on vessel traffic flow applying in traffic organization. The study on vessel traffic flow behavior characteristics is helpful to guide the evolution of the traffic flow, and it can make the vessel traffic flow more orderly and reasonably, so that it is significant to reduce the rate of the maritime traffic accident and improve the navigation efficiency.