In recent years, with the improvement of people’s living standards, organic products with health, ecology, safety advantages, have become a hot in consumer market. However, in the current market environment, the organic product was mixed, causing a crisis of confidence of consumers. Production processes are the ultimately problem. The organic certification is just beginning in China. Thus there is a greater risk when the certification bodies certificating the production process, affecting certification result. Aiming at the problems of lack of integrity and effectiveness of the organic vegetables production certification, and less of quantitative assessment method for the organic vegetables certification risk, according to the basic principle of catastrophe progression method and the national standard of organic product, combining with the production of organic vegetables, the organic vegetables certification risk evaluation index system was built, the three-tie architecture model of organic vegetables certification risk assessment was put forward based on catastrophe progression method, the qualitative factors were quantified, certification risk was assessed and the organic vegetables certification risk assessment system was designed based on catastrophe progression method. By testing the practical application of the system, the model can assess organic vegetables certification risk efficiently and show the key certification risk impact point at the same time. The research improved the integrity and effectiveness of organic vegetables certification, provided risk management recommendations for the management of organic vegetable production, and provided scientific basis for the relevant functional departments to supervise the production of organic vegetables.