To address the challenges of ship navigation decision-making in the water area where the navigable width of the estuary deep channel changes, taking the north channel deep waterway of the Yangtze River estuary as an example, research is conducted on the key scientific issues such as environmental digital twin, navigation rule integration, ship maneuverability limitation, and collision avoidance mechanism in special water area. First, the environmental components are classified, modeled, and implented into an environmental digital twin. Navigation requirements are summarized, quantitatively analyzed, and integrated into the decision-making process. A control and process prediction method for the nonlinear maneuvering characteristics of the own ship is proposed. Then, collision avoidance mechanism specific to the ship behavior characteristics of the research water area is explored. A method for obtaining the feasible heading and speed range is established, and a dynamic navigation decision-making method is proposed, which is capable of adapting to the system residual error and the random motion of the target ship under multiple constraints. In preset scenarios, the method proposed ensures all safe passage targets with adjustments of course 7° to starboard, course 2° to starboard with a telegraph order reduction to forward 1, course 5° to starboard with a telegraph order reduction to forward 1 at 241 s, 1 484 s, and 4 119 s respectively. The results show that the proposed method can accurately make navigation decisions, ensure collision avoidance, and perform route tracking in a timely manner.