Germplasm resource management is a basic work. It is heavy , complex and the workflow is long. It also contains large amount of relevant information to be dealed with. With more and more state's attention to germplasm resources ,and the development of the third national census and collection of crop germplasm resources, collection and preservation of germplasm resources in the future will further increase. At the same time, with the further improvement of breeding level and breeding technology in China, the demand for germplasm resources is increasing. As a result, the quantity of germplasm resources in and out of the germplasm resource bank increased exponentially. So we need modern management system to manage germplasm resources. It will make the management of crop germplsm resources be efficient and standardized. Shanghai crop germplasm resources management information system was established by Shanghai Agribiological Gene Center .It based on more than 10 years of operating experience. In this paper, the construction principle, overall design framework and main function modules of the management information system are introduced in detail. And emphatically introduces the aspects of storehouse management, seed information management, seed import and export management, seed early warning, summary statistics, user management, feedback management and so on. It could provide the reference for other germplasm resource bank to establish the similar management system.