The contributions of crop germplasm resources to food security depend on their conservation and accessibility for use. The automated warehouse has begun to be applied to the ex situ preservation of crop germplasm resources in the crop genebank. Identifying the proper storage scheme for potentially hundreds of thousands of seeds is a primary task that faces the crop genebank manager during the design of a new automated crop genebank. There are mainly three areas to focus on, hardware and software, seeds storage assignment policy and seeds labelling technology. This paper aims to propose automated crop genebank storage schemes for two kinds of crop genebank (the long-term crop genebank and the middle-term crop genebank), which supports managers in determining the technologies that can be applied in the automated crop genebank. Firstly, the selection of hardware and software should be based on the functional orientation of the long-term crop genebank and the middle-term crop genebank. Secondly, for the seed storage assignment policy, the sequential storage assignment is designed for the long-term genebank while the cache storage assignment is developed for the middle-term genebank. Finally, a QR code labelling technology based on image recognition is designed for both the long-term crop genebank and the middle-term crop genebank.