Practical Byzantine Fault Tolerance (PBFT) consensus mechanism shows a great potential to break the performance bottleneck of the Proof-of-Work (PoW)-based blockchain systems, which typically support only dozens of transactions per second and require minutes to hours for transaction confirmation. However, due to frequent inter-node communications, PBFT mechanism has a poor node scalability and thus it is typically adopted in small networks. To enable PBFT in large systems such as massive Internet of Things (IoT) ecosystems and blockchain, in this article, a scalable multi-layer PBFT-based consensus mechanism is proposed by hierarchically grouping nodes into different layers and limiting the communication within the group. We first propose an optimal double-layer PBFT and show that the communication complexity is significantly reduced.