Based on the stress-strain data collected by a CSSMAS (container ship structure monitoring and analyzing system) onboard a container vessel, stress-strain responses of the ship's structure in high wave were analyzed and illustrated for the identification of reasonable safe course sections. Besides the ship's structure safety, the maneuvering convenience is also deemed as a main concern which influences the safety of vessels in heavy waves. In order to develop a comprehensive guidance in adverse weather condition, the basic requirements on maneuvering convenience for vessels in storm were further discussed. In combination of the two requirements, namely structure health and maneuvering convenience, a proposed operational method was thus developed, which was an amendment to the traditional navigational method for ship in extreme weather. At the end of this paper, an example of optimal course planning in bad weather was illustrated by using the operational method proposed.