In order to achieve the digital management of null-pollution agricultural products certification and by adopting techniques such as Web Service, distributed database and workflow, this essay has completed the design and development of the system based on the J2EE platform. It includes certification data service subsystem, declare subsystem and certification workflow management subsystem. This system can highly automize and standardize the key link of origin and product certification such as the review of filing materials, site inspection and environment detection. It can automatically generate filing materials, inspection report and evaluation report. It has the function of sending documents among certification management departments at various levels and storing them respectively. This system has speed up the agricultural products origin and product certification integration process and realized standardized and digitalized management of certification work.