According to actual of cow epidemic disease diagnosis, bidirectional reasoning scheme based on the symptom both characterization and autopsy is proposed, which is based on inexact reasoning of certainty factor. The process of both construction the knowledge database for cow epidemic disease diagnosis and the inexact reasoning based on certainty factor are amplified. A web-based system on the platform of Tomcat+JSP+MySQL+DWR about the cow epidemic disease diagnosis is realized base on MVC. By testing, it is shown that the monitoring 21 kinds of cow epidemic disease in China can be accurately diagnosed, basically. It can be widely used in breeding aquatics village, breeding farm, raising households and so on. It will play a positive role to prevent and control the cow epidemic disease.