In this paper, a novel ship domain model termed quaternion ship domain (QSD) is proposed. Unlike other ship domains, the proposed QSD is more dependable and more flexible for navigators to use to make decisions. The main characteristics are that: the domain size is determined by the quaternion including four radii, i.e. fore, aft, starboard and port, which sufficiently take factors affecting the domain (i.e. ship manoeuvring capability, speeds and courses, etc.) into account; and that the domain shape is modelled by another parameter which makes the QSD more flexible since the ship boundary could not only be linear or nonlinear, but also be thin or fat. In order to reasonably relate the proposed QSD to practical applications, i.e. collision risk assessment, collision avoidance and trajectory planning, etc., a fuzzy QSD (FQSD) has been developed by using fuzzy sets. As a result, fuzzy boundaries rather than crisp ones in the FQSD are more practical and more convenient for navigators to understand and judge since uncertainty and fuzzy information have been merged into the FQSD. Furthermore, concepts of longitudinal and lateral risk based on the FQSD have been introduced to estimate the spatial collision risk (SCR) for the ships encountered. Finally, several computer simulations have been conducted on various encounter situations and comparative studies with other ship domains have been comprehensively analyzed. Simulation results demonstrate that the proposed QSD is more effective and more flexible than other ship domains, and that the intelligent SCR based on the FQSD are reasonable and dependable.