Clothes that are comfortable and functional are important in daily life; however, the manufacture of fluorine‐free functional fabrics with excellent waterproofness and breathability using simple and environmentally friendly methods still presents several technical challenges. Currently, the ultraviolet (UV) radiation‐initiated thiol‐ene click reaction is used for the construction of hydrophobic surfaces due to its high efficiency and the mild reaction conditions involved. Therefore, in this work, the electrospinning technique and the UV‐initiated thiol‐ene click reaction to introduce hydrophobic octadecanethiol (thiol) and 2,4,6,8‐tetramethyl‐2,4,6,8‐tetra‐vinylcyclotetrasiloxane (TMTVSi) into the silicon‐based polyurethane/polymethyl methacrylate (Si‐PU/PMMA) nanofibrous membranes is combined. After UV irradiation, the sulfhydryl groups of the thiol react with the carbon–carbon double bond of the TMTVSi, resulting in cross‐linking between the nanofibers. The fluorine‐free Si‐PU/PMMA/TMTVSi‐thiol‐30 waterproof and breathable electrospun nanofibrous membranes are observed to show excellent properties, which include a hydrostatic pressure of 64.43 kPa, water vapor transmittance (WVT) rate of 7879 g m−2 d−1, and robust tensile stress of 10.04 MPa, all of which enable the membrane to be widely used in the field of protective garments and oil–water separation.