Recently, food safety incidents have occurred consistently in China. Accordingly, much attention has been given to the establishment and development of food safety risk assessment in China. In this article risk assessment research status of food borne pathogenic microorganisms, including applications of food safety risk assessment techniques to the storage, transportation, distribution of aquatic products, and new sterilization technology to lower risks caused by pathogenic microorganism in aquatic products, was introduced briefly. Based on the analysis of differences of pathogenic microorganism risk assessment in aquatic products between other countries and China, some views and suggestions about risk assessment researches in future were put forward.