Abstract: Aiming at the key issue of agricultural product quality safety certification, the integrated workflow of origin cognizance and product certification of pollution-free agricultural products was studied so as to construct a digital certification system of pollution-free agricultural products from the perspective of information technology, with the aim of achieving normalization of the certification flow and improving working efficiency. Through the analysis of certification activities, the authors established the domain environment of two-level nodes of the certification flow, constructed centralized distributed topological structure among the node domains, designed system functions flow under the distributed environment, and discussed the key technologies; Declarer, detection mechanism and administrative departments at all levels oriented digital certification system of distributed pollution-free agricultural products was developed with the combined use of meta-data, workflow and Web Service technology. The system provides the functions of declaration management, certification workflow management, and certification information resource service to achieve the electronic management of full flow and orientation of pollution-free agricultural products certification. After pilot application in Henan Province and the Ministry of Agriculture, the results show that the system has achieved cross-sectoral and cross-boundary teamwork, as well as high efficient management of certification information, having a good prospect of application and popularization.