The unique infinite self-renewal ability and multidirectional differentiation potential of stem cells provide a strong support for the clinical treatment. In light of the growing demands for stem cell storage, how to ensure personal privacy security and comply with strict ethical supervision requirements is particularly important. In order to solve the problem of low security of traditional encryption algorithm, we proposed a double encryption protection (DEP) algorithm for stem cell bank privacy data based on improved AES and chaotic encryption technology. Firstly, we presented the hash value key decomposition algorithm, through the hash value dynamic coding, cyclic shift, conversion calculation to get the key of each subsystem in the built algorithm. Secondly, DEP algorithm for privacy data is realized with two level of encryption. The first level of encryption protection algorithm used AES as the main framework, adding dynamic coding and byte filling based on DNA coding, and carries out dynamic shift of rows and simplified mixing of columns. The second level of encryption protection algorithm conducted random encoding, operation, diffusion and decoding based on the results of our proposed sequence conversion algorithm. Finally, we raised two evaluation indexes, the number of characters change rate (NCCR) and the unified average change intensity of text (UACIT) to measure the sensitivity of encryption algorithms to changes in plain information. The experimental results of using DEP shown that the average values of histogram variance, information entropy, NCCR and UACIT are116.7883, 7.6688, 32.52% and 99.67%, respectively. DEP algorithm has a large key space, high key sensitivity, and enables dynamic encryption of private data in stem cell bank. The encryption scheme provided in this study ensures the security of the private information of stem cell bank in private cloud environment, and also provides a new method for the encryption of similar high confidentiality data.