With the popularity of cloud storage, increasingly more files are stored in cloud storage servers rather than in users’ computers, which makes users lose absolute control over the data and data security difficult to guarantee. To solve this problem, this study proposes a secure cloud storage system. It is implemented in the user model and can be directly set up on the computer file system, with low requirements for computer hardware and software. Functions such as end-to-end data encryption protection, integrity check, and access control are provided through the block encryption algorithm and the design of Merkle-B+ tree. The system is simple to use and completely transparent to users, with a reduced user threshold. The test results of this system show that when it is mounted on the network file system (NFS), its input/output (I/O) performance in a large file environment is reduced by about 5%, which indicates that the system has good performance in addition to ensured user data security and system ease of use.