Ultrasmall metal nanoclusters (MNCs, <2 nm) are emerging materials with unique properties, yet synthesizing non-coinage MNCs, especially high-melting-point elements like Fe, Ti, and Mn, remains challenging due to the lack of mild, general strategies, hindering applications such as electrochemical desalination. Herein, a universal "pore-mediated vapor diffusion" (PVD) method is reported to synthesize sub-nanometer Fe NCs (0.8 nm) within mesoporous carbon spheres, tackling the critical bottleneck issue of faradaic capacitive deionization (FDI)-a promising approach for mitigating global water scarcity. This approach bypasses high-temperature requirements and extends to other refractory metals. As a FDI anode, the Fe NC electrode achieves a record salt adsorption capacity of 116.83 mgCl g-1, an ultrahigh rate of 0.57 mgCl g-1 s-1, and exceptional stability (86.47% retention after 200 cycles). The sub-nanometer structure enables ultrafast ion diffusion and stress mitigation, overcoming persistent kinetic and stability limitations in FDI. Through operando X-ray spectroscopy and DFT, the chloride storage mechanism is identified as a conversion reaction (Fe NCs + Cl- ⇌ FeOCl), resolving key ambiguities at the atomic level in Fe electrochemistry. This work provides a versatile synthesis platform for non-coinage MNCs and atomic-level mechanistic insights, advancing next-generation desalination technologies.