Fabricating breakthrough materials capable of desalinating seawater and brine with high selectivity and low energy consumption is crucial for addressing global water and energy challenges. We report here the desalination capability of ultra-thin polymeric films with subnanometer pores synthesized through the polymerization of fluorinated trichlorosilane monomers and diamine-based monomers. The combination of subnanometer pore size, submicron thickness, and superhydrophobicity facilitates efficient liquid-to-vapor phase change in the membrane distillation process, enabling effective desalination performance. The thin-films demonstrate high salt rejection (99.8%), complete boron rejection, and water fluxes of 40 L.m−2.h−1 (1.88 kWh.m−3, WRRsp 0.32%) and 238 L.m−2.h−1 (20.65 kWh.m−3, WRRsp 3.87%) for seawater at 25 °C and 60 °C, respectively. For the desalination of real seawater reverse osmosis brine at 25 °C, the thin-films maintain 12 L.m−2.h−1 (4.4 kWh.m−3, WRRsp 0.09%) under comparable conditions. Their polymeric nature, chlorine resistance, and low energy requirements, indicate a potential for scalable and sustainable desalination systems.