A ship that is not under control (NUC) is a typical incident that poses serious problems when in confined waters close to shore. The emergency response to NUC ships is to select the best risk control options, which is a challenge in restricted conditions (e.g., time limitation, resource constraint, and information asymmetry), particularly in inland waterway transportation. To enable a quick and effective response, this article develops a three-stage decision-making framework for NUC ship handling. The core of this method is (1) to propose feasible options for each involved entity (e.g., maritime safety administration, NUC ship, and ships passing by) under resource constraint in the first stage, (2) to select the most feasible options by comparing the similarity of the new case and existing cases in the second stage, and (3) to make decisions considering the cooperation between the involved organizations by using a developed Bayesian network in the third stage. Consequently, this work provides a useful tool to achieve well-organized management of NUC ships.