To improve the efficiency of secure disk encryption, expand the disk storage space, and avoid attacks that limit the encryption effect, this study designed a secure disk encryption system based on embedded control and advanced encryption standard (AES) algorithm. First, the overall architecture of a secure disk encryption system was designed. Among them, the Nios embedded processor plays the role of control core and data processing core unit, which is mainly used to coordinate the instruction transmission, data transmission, encryption, and decryption operations when the host accesses the hard disk data. Next, the working principles of the hard disk encryption card, encryption chip module, hard disk encryption module, programmed I/O interface, and cache module are analyzed. Based on the hardware design, analyze the basic structure of AES algorithm and use the AES algorithm to achieve secure disk encryption. Experimental results showed that the highest safety factor of the disk was 0.95, the maximum storage space of the disk could reach 3,700 MB, and the longest encryption time of the secure disk was only 6.05s. It can achieve comprehensive identification of message tampering attacks, denial of service attacks, password intrusion attacks, node attacks, and pseudo-remote attacks, indicating that the application performance of the system is good.