An Fe-based heterogeneous catalyst is an attractive Fenton-like catalyst for phenol synthesis due to many advantages. Nevertheless, it is challenging to control the particle size in various high-loading Fe-based materials, which limits its activity and selectivity. In this work, ultra-small Fe clusters embedded in a 3D porous interconnected open-framework g-C3N4 (denoted FeNx/CCN) were successfully fabricated by the combination of a mechanochemical reaction with one-step pyrolysis. Various characterization results showed that ultra-small Fe clusters with a high loading of 32% were uniformly distributed in the hierarchical porous carbon nitride, which offered an access for faster transportation of charge carriers. Fe sites were probably coordinated with carbon nitride by Fe2+–C≡ N–Fe3+ and Fe–Nx bonding. High-density Fe clusters could provide abundant active sites and improve the light absorption and the activating ability of H2O2. By taking advantage of semiconductor functions in combination with a rich porous structure and high-density active sites, the novel Fe cluster catalyst exhibited high activity and stability in phenol synthesis, with a maximum phenol yield of 28.1% in visible light. Combining the experimental results with Fenton chemistry, we proposed a possible photocatalytic reaction mechanism. Our work will give valuable information on the development of active metal cluster nanocatalysts for organic synthesis.