The Internet is transitioning from Web3 toward Web4, where autonomous agents serve as independent economic actors. These agents can now hold crypto wallets, execute on-chain trades, and pay for external API calls. This transition calls for a new infrastructure stack capable of supporting key agent operations, including agent-to-tool interaction, agent-to-agent payments, and verifiable agent identity, represented by emerging protocols such as the Model Context Protocol, x402, and EIP-8004. Despite growing industrial interest in these protocols, the real-world Web4 agent ecosystem remains largely underexplored. To bridge this gap, we conduct the first large-scale empirical study of the Web4 ecosystem. Specifically, our study targets three interconnected questions: how Web4 agents are deployed and used in practice; what engineering challenges developers face when building Web4 agents; how current project communities respond to these challenges. To answer these questions, we analyze 99,448 multi-chain identity registrations, 317,596,323 transaction logs, the source code of 341 MCP projects, and 349 filtered GitHub issues. Our findings reveal that autonomous agents have established a highly active machine-to-machine payment economy, processing millions of daily transactions. However, this growth is built on immature infrastructure, including identity/authorization practice, cross-environment operation, and payment interoperability. Our follow-up analysis shows that community responses are visible but unevenly distributed across repositories, and payment interoperability remains the most persistent unresolved bottleneck. Overall, this study reveals a critical gap between the rapid growth of the Web4 agent economy and its fragile underlying infrastructure, highlighting future directions for building a more secure Web4 agent ecosystem.

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