Embedded system security is an inevitable requirement for ensuring the security of industrial control systems. However, the cost-limited hardware resources may not be able to effectively support the additional calculation overhead brought by the application of encryption algorithms. In this paper, we focusd on the feasibility of the migration of encryption algorithms for embedded systems and the impact on the system performance. And a performance benchmark method of encryption algorithm for embedded system was proposed to realize the connection between the system side and the cipher side by constructing equivalent metrics. The experiment carried out by this method covered the performance benchmark of encryption algorithms with different configurations including domestic encryption algorithm and lightweight cryptography algorithm with running time delay, throughput and system resource utilization as metrics. The experimental results show that the increase in the encryption algorithm key length will increase the algorithm execution delay, and the increase in the algorithm packet size will accelerate the algorithm's running speed. The performance impact caused by the use of different encryption modes will vary with the encryption algorithm. Direct deployment of encryption algorithm to detect system index values during task execution can simplify the measurement and is more practical than the application of other abstract models in industrial scene.