Recently, a basic pattern of coast seaway system networking has been established in China. As a result, a large number of precautionary areas will be gradually established. Because of the high frequency of ships' encounters and accidents, these precautionary areas have been a weak but important facet of ships' routeing. Navigational Traffic Conflict Technique (NTCT) was introduced to quantitatively evaluate the safety of precautionary areas. Focusing on traffic conflict, the calculation method of navigational traffic conflict points is discussed, and a comparison analysis of the two editions (2002 and 2008) of Yangtze estuary ships’ routeing is performed. Then the automatic acquisition system of navigational traffic conflict data that can be used in the quantitative analysis of the influence degree of a single traffic flow on the whole precautionary area safety is developed, and the left-turning traffic flows of Yangtze estuary ships’ routeing precautionary areas B are taken as an example. This article establishes a foundation for the precautionary area safety analysis system, and provides the decision basis for policy making in optimisation of geometric design and traffic organisation of precautionary areas.