The permissioned blockchain system has recently become popular in a wide range of scenarios, such as artificial intelligence, financial applications and the Internet of things, due to its dominance in terms of distribution, decentralization, reliability and security. However, the Practical Byzantine Fault-Tolerant (PBFT) algorithm, which is currently adopted in such systems, sparks communication bottlenecks when the number of consensus nodes increases sharply, which seriously hinders large-scale applications. In this paper, we propose a scalable dynamic multi-agent hierarchical PBFT algorithm (SDMA-PBFT), which reduces the communication costs from O(n2) to O( n × k × log k n ). Specifically, SDMA-PBFT forms multiple autonomous systems at each agent node in which message multicasting can be efficiently carried out and the internal voting results can be effectively collected. Therefore, the design of these agent nodes facilitates the in-and-out operations of consensus nodes in the blockchain system. Simulation results show that our proposed algorithm substantially outperforms the PBFT algorithm in terms of latency. Hence, it can be applied to the permissioned blockchain system effectively and efficiently.