It is of great importance for any vessel under way, especially in rough sea, to be maneuvered safely with proper seakeeping performance. In this paper, the author aims to develope a navigational safety evaluation system in rough sea by analyzing ship's with the theory of wave spectrum using random process analysis and the theory of evaluating the seakeeping performance. The scope and the method of this study are as follows ; (1) Modelized typhoon mathematically to represent the sea condition in rough sea. (2) Estimated sea conditions by getting wave spectrum, supposing that the wave by typhoon is fully developed short crest irregular wave. (3) Defined evaluation factor of vessel's seakeeping performance and obtained response amplitude operators thereby. (4) Obtained the response spectrum of factors on seakeeping performance. (5) Defined and obtained evaluation index, dangerousness, relative and maximum dangerousness of factors on seakeeping performance. (6) Analyzed the calculated dangerousness of evaluation index and picked the vertical acceleration out of 7 factors as the presentative factor on seakeeping performance. (7) Carrid out the judgement of danger by obtaining dangerousness value according to steaming hour, course alteration and speed change. By synthesizing the above items, the authors suggests a computer model of navigational safety evaluation system and examined the validity of the model by computer simulation.