The invention belongs to the technical field of computer storage, and provides a safe storage method based on a plurality of cloud storage systems and a system thereof. The method and the system can achieve the purpose that in the plurality of existing cloud storage systems, safety of data and metadata can be guaranteed at the same time. The safe storage method comprises a step of data writing operation and a step of data reading operation, wherein the step of data writing operation comprises the sub-steps of data partitioning, data encryption, redundancy encoding, digital signature, sharing processing, and data storage. The step of data reading operation comprises the sub-steps of metadata partition file decryption, digital signature inspection, redundancy decoding and cipher text data block decryption. The safe storage system comprises an encryption and decryption coding module, a redundancy encoding module, a secret sharing module and a digital signature module. By means of the method and the system, metadata privacy and high availability can be guaranteed, and meanwhile, a user does not need to store any metadata information for indexing and data query.