Abstract2D materials have attracted considerable attention in the past decades for their unique properties, making the understanding of their nucleation process key to effective synthesis. Traditional explanations of thin‐film growth, focusing on the competition between atom interactions at the interface and within layers, often fall short of explaining real experimental results. Herein, a penetrated nucleation mechanism is proposed for 2D materials growth on metal substrates, taking into account the role of metal substrate atoms. This approach leads to a better understanding of how the surface shape evolves in two specific ways during growth in real experimental findings. Supported by detailed first‐principles simulations of boron on metal substrates and thermodynamic analyses of other studies involving metals and nonmetals, the above‐proposed mechanism is validated. Moreover, a broad strategy for growing large‐scale 2D materials on metal surfaces without creating undesired alloy layers is also presented, by adjusting the interfacial interactions by surface passivation, validated by existing experiments.