Embedded systems have attracted great attention with their unique information processing ability and human-computer interaction ability, and how to improve the processing efficiency of embedded systems for low-capacity storage units has become a key topic of current research. Based on the data storage structure characteristics and hardware devices of embedded systems, we complete the task of storage structure design for embedded systems and describe the interaction mechanism of Cache storage mode and low-capacity storage mode. Using the POSE algorithm, we optimize the execution efficiency and module energy overhead in the storage structure of the embedded system and test and optimize the embedded system. The low-capacity storage mode has fewer physical block erasures than the Cache storage mode, and the response time is 15-50 ms less. Similarly, the PEOS algorithm has advantages in the optimization of the energy overhead of the embedded system, which ranges from 0 to 0.23 × 104. This study can effectively improve the execution efficiency and energy overhead of the storage, which is of great significance for its further development.