Blockchain has the characteristics of decentralization, security, reliability, and immutability, and has received widespread attention recently. Merkle tree is the core component of the block, accounting for more than 96% of the block storage. It is mainly used to handle the problem of simplified payment verification in Blockchain transactions. Therefore, choosing the appropriate Merkle tree structure will greatly affect the performance of the Blockchain. However, there is no public platform to analyze and verify the performance of Merkle tree under different Blockchain systems at present. In this study, we propose a set of related performance evaluation and analysis indexes in terms of storage, verification, and build time. The performance of the Merkle tree of the three mainstream Blockchains of Bitcoin, Ethereum, and Hyperledger is evaluated. The index and evaluation method proposed in this study not only provides quantitative data support for further research on Merkle trees, but also provides guidance for Blockchain practitioners in choosing Merkle tree structures.